diff --git a/test/e2e/e2e_test.go b/test/e2e/e2e_test.go
index 373e038cc0c..a9051577450 100644
--- a/test/e2e/e2e_test.go
+++ b/test/e2e/e2e_test.go
@@ -61,9 +61,13 @@ import (
 var viperConfig = flag.String("viper-config", "", "The name of a viper config file (https://github.com/spf13/viper#what-is-viper). All e2e command line parameters can also be configured in such a file. May contain a path and may or may not contain the file suffix. The default is to look for an optional file with `e2e` as base name. If a file is specified explicitly, it must be present.")
 
 func init() {
-	// Register framework flags, then handle flags and Viper config.
+	// Register framework and test flags, then parse flags.
 	framework.HandleFlags()
-	if err := viperconfig.ViperizeFlags(*viperConfig, "e2e"); err != nil {
+
+	// Now that we know which Viper config (if any) was chosen,
+	// parse it and update those options which weren't already set via command line flags
+	// (which have higher priority).
+	if err := viperconfig.ViperizeFlags(*viperConfig, "e2e", flag.CommandLine); err != nil {
 		fmt.Fprintln(os.Stderr, err)
 		os.Exit(1)
 	}
diff --git a/test/e2e/framework/config/config.go b/test/e2e/framework/config/config.go
index 1cd4a052f62..5fa37bcae73 100644
--- a/test/e2e/framework/config/config.go
+++ b/test/e2e/framework/config/config.go
@@ -15,11 +15,22 @@ limitations under the License.
 */
 
 // Package config simplifies the declaration of configuration options.
-// Right now the implementation maps them directly command line
-// flags. When combined with test/e2e/framework/viper in a test suite,
-// those flags then can also be read from a config file.
+// Right now the implementation maps them directly to command line
+// flags. When combined with test/e2e/framework/viperconfig in a test
+// suite, those flags then can also be read from a config file.
 //
-// Instead of defining flags one-by-one, developers annotate a
+// The command line flags all get stored in a private flag set. The
+// developer of the E2E test suite decides how they are exposed. Options
+// include:
+// - exposing as normal flags in the actual command line:
+//   CopyFlags(Flags, flag.CommandLine)
+// - populate via test/e2e/framework/viperconfig:
+//   viperconfig.ViperizeFlags("my-config.yaml", "", Flags)
+// - a combination of both:
+//   CopyFlags(Flags, flag.CommandLine)
+//   viperconfig.ViperizeFlags("my-config.yaml", "", flag.CommandLine)
+//
+// Instead of defining flags one-by-one, test developers annotate a
 // structure with tags and then call a single function. This is the
 // same approach as in https://godoc.org/github.com/jessevdk/go-flags,
 // but implemented so that a test suite can continue to use the normal
@@ -84,10 +95,23 @@ import (
 	"unicode/utf8"
 )
 
-// CommandLine is the flag set that AddOptions adds to. Usually this
-// is the same as the default in the flag package, but can also be
-// something else (for example during testing).
-var CommandLine = flag.CommandLine
+// Flags is the flag set that AddOptions adds to. Test authors should
+// also use it instead of directly adding to the global command line.
+var Flags = flag.NewFlagSet("", flag.ContinueOnError)
+
+// CopyFlags ensures that all flags that are defined in the source flag
+// set appear in the target flag set as if they had been defined there
+// directly. From the flag package it inherits the behavior that there
+// is a panic if the target already contains a flag from the source.
+func CopyFlags(source *flag.FlagSet, target *flag.FlagSet) {
+	source.VisitAll(func(flag *flag.Flag) {
+		// We don't need to copy flag.DefValue. The original
+		// default (from, say, flag.String) was stored in
+		// the value and gets extracted by Var for the help
+		// message.
+		target.Var(flag.Value, flag.Name, flag.Usage)
+	})
+}
 
 // AddOptions analyzes the options value and creates the necessary
 // flags to populate it.
@@ -102,6 +126,11 @@ var CommandLine = flag.CommandLine
 // It panics when it encounters an error, like unsupported types
 // or option name conflicts.
 func AddOptions(options interface{}, prefix string) bool {
+	return AddOptionsToSet(Flags, options, prefix)
+}
+
+// AddOptionsToSet is the same as AddOption, except that it allows choosing the flag set.
+func AddOptionsToSet(flags *flag.FlagSet, options interface{}, prefix string) bool {
 	optionsType := reflect.TypeOf(options)
 	if optionsType == nil {
 		panic("options parameter without a type - nil?!")
@@ -109,11 +138,11 @@ func AddOptions(options interface{}, prefix string) bool {
 	if optionsType.Kind() != reflect.Ptr || optionsType.Elem().Kind() != reflect.Struct {
 		panic(fmt.Sprintf("need a pointer to a struct, got instead: %T", options))
 	}
-	addStructFields(optionsType.Elem(), reflect.Indirect(reflect.ValueOf(options)), prefix)
+	addStructFields(flags, optionsType.Elem(), reflect.Indirect(reflect.ValueOf(options)), prefix)
 	return true
 }
 
-func addStructFields(structType reflect.Type, structValue reflect.Value, prefix string) {
+func addStructFields(flags *flag.FlagSet, structType reflect.Type, structValue reflect.Value, prefix string) {
 	for i := 0; i < structValue.NumField(); i++ {
 		entry := structValue.Field(i)
 		addr := entry.Addr()
@@ -134,12 +163,12 @@ func addStructFields(structType reflect.Type, structValue reflect.Value, prefix
 			// Entries in embedded fields are treated like
 			// entries, in the struct itself, i.e. we add
 			// them with the same prefix.
-			addStructFields(structField.Type, entry, prefix)
+			addStructFields(flags, structField.Type, entry, prefix)
 			continue
 		}
 		if structField.Type.Kind() == reflect.Struct {
 			// Add nested options.
-			addStructFields(structField.Type, entry, name)
+			addStructFields(flags, structField.Type, entry, name)
 			continue
 		}
 		// We could switch based on structField.Type. Doing a
@@ -153,33 +182,33 @@ func addStructFields(structType reflect.Type, structValue reflect.Value, prefix
 		case *bool:
 			var defValue bool
 			parseDefault(&defValue, name, def)
-			CommandLine.BoolVar(ptr, name, defValue, usage)
+			flags.BoolVar(ptr, name, defValue, usage)
 		case *time.Duration:
 			var defValue time.Duration
 			parseDefault(&defValue, name, def)
-			CommandLine.DurationVar(ptr, name, defValue, usage)
+			flags.DurationVar(ptr, name, defValue, usage)
 		case *float64:
 			var defValue float64
 			parseDefault(&defValue, name, def)
-			CommandLine.Float64Var(ptr, name, defValue, usage)
+			flags.Float64Var(ptr, name, defValue, usage)
 		case *string:
-			CommandLine.StringVar(ptr, name, def, usage)
+			flags.StringVar(ptr, name, def, usage)
 		case *int:
 			var defValue int
 			parseDefault(&defValue, name, def)
-			CommandLine.IntVar(ptr, name, defValue, usage)
+			flags.IntVar(ptr, name, defValue, usage)
 		case *int64:
 			var defValue int64
 			parseDefault(&defValue, name, def)
-			CommandLine.Int64Var(ptr, name, defValue, usage)
+			flags.Int64Var(ptr, name, defValue, usage)
 		case *uint:
 			var defValue uint
 			parseDefault(&defValue, name, def)
-			CommandLine.UintVar(ptr, name, defValue, usage)
+			flags.UintVar(ptr, name, defValue, usage)
 		case *uint64:
 			var defValue uint64
 			parseDefault(&defValue, name, def)
-			CommandLine.Uint64Var(ptr, name, defValue, usage)
+			flags.Uint64Var(ptr, name, defValue, usage)
 		default:
 			panic(fmt.Sprintf("unsupported struct entry type %q: %T", name, entry.Interface()))
 		}
diff --git a/test/e2e/framework/config/config_test.go b/test/e2e/framework/config/config_test.go
index d6856e696ad..a5e8b495d3d 100644
--- a/test/e2e/framework/config/config_test.go
+++ b/test/e2e/framework/config/config_test.go
@@ -17,6 +17,7 @@ limitations under the License.
 package config
 
 import (
+	"bytes"
 	"flag"
 	"testing"
 	"time"
@@ -26,12 +27,12 @@ import (
 )
 
 func TestInt(t *testing.T) {
-	CommandLine = flag.NewFlagSet("test", 0)
+	flags := flag.NewFlagSet("test", 0)
 	var context struct {
 		Number int `default:"5" usage:"some number"`
 	}
 	require.NotPanics(t, func() {
-		AddOptions(&context, "")
+		AddOptionsToSet(flags, &context, "")
 	})
 	require.Equal(t, []simpleFlag{
 		{
@@ -39,18 +40,18 @@ func TestInt(t *testing.T) {
 			usage:    "some number",
 			defValue: "5",
 		}},
-		allFlags(CommandLine))
+		allFlags(flags))
 	assert.Equal(t, 5, context.Number)
 }
 
 func TestLower(t *testing.T) {
-	CommandLine = flag.NewFlagSet("test", 0)
+	flags := flag.NewFlagSet("test", 0)
 	var context struct {
 		Ähem      string
 		MixedCase string
 	}
 	require.NotPanics(t, func() {
-		AddOptions(&context, "")
+		AddOptionsToSet(flags, &context, "")
 	})
 	require.Equal(t, []simpleFlag{
 		{
@@ -60,16 +61,16 @@ func TestLower(t *testing.T) {
 			name: "ähem",
 		},
 	},
-		allFlags(CommandLine))
+		allFlags(flags))
 }
 
 func TestPrefix(t *testing.T) {
-	CommandLine = flag.NewFlagSet("test", 0)
+	flags := flag.NewFlagSet("test", 0)
 	var context struct {
 		Number int `usage:"some number"`
 	}
 	require.NotPanics(t, func() {
-		AddOptions(&context, "some.prefix")
+		AddOptionsToSet(flags, &context, "some.prefix")
 	})
 	require.Equal(t, []simpleFlag{
 		{
@@ -77,11 +78,11 @@ func TestPrefix(t *testing.T) {
 			usage:    "some number",
 			defValue: "0",
 		}},
-		allFlags(CommandLine))
+		allFlags(flags))
 }
 
 func TestRecursion(t *testing.T) {
-	CommandLine = flag.NewFlagSet("test", 0)
+	flags := flag.NewFlagSet("test", 0)
 	type Nested struct {
 		Number1 int `usage:"embedded number"`
 	}
@@ -96,7 +97,7 @@ func TestRecursion(t *testing.T) {
 		}
 	}
 	require.NotPanics(t, func() {
-		AddOptions(&context, "")
+		AddOptionsToSet(flags, &context, "")
 	})
 	require.Equal(t, []simpleFlag{
 		{
@@ -110,38 +111,39 @@ func TestRecursion(t *testing.T) {
 			defValue: "0",
 		},
 	},
-		allFlags(CommandLine))
+		allFlags(flags))
 }
 
 func TestPanics(t *testing.T) {
+	flags := flag.NewFlagSet("test", 0)
 	assert.PanicsWithValue(t, `invalid default "a" for int entry prefix.number: strconv.Atoi: parsing "a": invalid syntax`, func() {
 		var context struct {
 			Number int `default:"a"`
 		}
-		AddOptions(&context, "prefix")
+		AddOptionsToSet(flags, &context, "prefix")
 	})
 
 	assert.PanicsWithValue(t, `invalid default "10000000000000000000" for int entry prefix.number: strconv.Atoi: parsing "10000000000000000000": value out of range`, func() {
 		var context struct {
 			Number int `default:"10000000000000000000"`
 		}
-		AddOptions(&context, "prefix")
+		AddOptionsToSet(flags, &context, "prefix")
 	})
 
 	assert.PanicsWithValue(t, `options parameter without a type - nil?!`, func() {
-		AddOptions(nil, "")
+		AddOptionsToSet(flags, nil, "")
 	})
 
 	assert.PanicsWithValue(t, `need a pointer to a struct, got instead: *int`, func() {
 		number := 0
-		AddOptions(&number, "")
+		AddOptionsToSet(flags, &number, "")
 	})
 
 	assert.PanicsWithValue(t, `struct entry "prefix.number" not exported`, func() {
 		var context struct {
 			number int
 		}
-		AddOptions(&context, "prefix")
+		AddOptionsToSet(flags, &context, "prefix")
 	})
 
 	assert.PanicsWithValue(t, `unsupported struct entry type "prefix.someNumber": config.MyInt`, func() {
@@ -149,12 +151,28 @@ func TestPanics(t *testing.T) {
 		var context struct {
 			SomeNumber MyInt
 		}
-		AddOptions(&context, "prefix")
+		AddOptionsToSet(flags, &context, "prefix")
 	})
 }
 
+type TypesTestCase struct {
+	name      string
+	copyFlags bool
+}
+
 func TestTypes(t *testing.T) {
-	CommandLine = flag.NewFlagSet("test", 0)
+	testcases := []TypesTestCase{
+		{name: "directly"},
+		{name: "CopyFlags", copyFlags: true},
+	}
+
+	for _, testcase := range testcases {
+		testTypes(t, testcase)
+	}
+}
+
+func testTypes(t *testing.T, testcase TypesTestCase) {
+	flags := flag.NewFlagSet("test", 0)
 	type Context struct {
 		Bool     bool          `default:"true"`
 		Duration time.Duration `default:"1ms"`
@@ -167,8 +185,25 @@ func TestTypes(t *testing.T) {
 	}
 	var context Context
 	require.NotPanics(t, func() {
-		AddOptions(&context, "")
+		AddOptionsToSet(flags, &context, "")
 	})
+
+	if testcase.copyFlags {
+		original := bytes.Buffer{}
+		flags.SetOutput(&original)
+		flags.PrintDefaults()
+
+		flags2 := flag.NewFlagSet("test", 0)
+		CopyFlags(flags, flags2)
+		flags = flags2
+
+		copy := bytes.Buffer{}
+		flags.SetOutput(&copy)
+		flags.PrintDefaults()
+		assert.Equal(t, original.String(), copy.String(), testcase.name+": help messages equal")
+		assert.Contains(t, copy.String(), "some number", testcase.name+": copied help message contains defaults")
+	}
+
 	require.Equal(t, []simpleFlag{
 		{
 			name:     "bool",
@@ -205,14 +240,14 @@ func TestTypes(t *testing.T) {
 			defValue: "1234567890123456789",
 		},
 	},
-		allFlags(CommandLine))
+		allFlags(flags), testcase.name)
 	assert.Equal(t,
 		Context{true, time.Millisecond, 1.23456789, "hello world",
 			-1, -1234567890123456789, 1, 1234567890123456789,
 		},
 		context,
 		"default values must match")
-	require.NoError(t, CommandLine.Parse([]string{
+	require.NoError(t, flags.Parse([]string{
 		"-int", "-2",
 		"-int64", "-9123456789012345678",
 		"-uint", "2",
@@ -221,13 +256,13 @@ func TestTypes(t *testing.T) {
 		"-float64", "-1.23456789",
 		"-bool=false",
 		"-duration=1s",
-	}))
+	}), testcase.name)
 	assert.Equal(t,
 		Context{false, time.Second, -1.23456789, "pong",
 			-2, -9123456789012345678, 2, 9123456789012345678,
 		},
 		context,
-		"parsed values must match")
+		testcase.name+": parsed values must match")
 }
 
 func allFlags(fs *flag.FlagSet) []simpleFlag {
diff --git a/test/e2e/framework/test_context.go b/test/e2e/framework/test_context.go
index fdc2524435c..970ecfc4b3a 100644
--- a/test/e2e/framework/test_context.go
+++ b/test/e2e/framework/test_context.go
@@ -33,6 +33,7 @@ import (
 	cliflag "k8s.io/component-base/cli/flag"
 	"k8s.io/klog"
 	kubeletconfig "k8s.io/kubernetes/pkg/kubelet/apis/config"
+	e2econfig "k8s.io/kubernetes/test/e2e/framework/config"
 	e2elog "k8s.io/kubernetes/test/e2e/framework/log"
 )
 
@@ -230,7 +231,17 @@ type CloudConfig struct {
 var TestContext TestContextType
 
 // RegisterCommonFlags registers flags common to all e2e test suites.
-func RegisterCommonFlags() {
+// The flag set can be flag.CommandLine (if desired) or a custom
+// flag set that then gets passed to viperconfig.ViperizeFlags.
+//
+// The other Register*Flags methods below can be used to add more
+// test-specific flags. However, those settings then get added
+// regardless whether the test is actually in the test suite.
+//
+// For tests that have been converted to registering their
+// options themselves, copy flags from test/e2e/framework/config
+// as shown in HandleFlags.
+func RegisterCommonFlags(flags *flag.FlagSet) {
 	// Turn on verbose by default to get spec names
 	config.DefaultReporterConfig.Verbose = true
 
@@ -240,117 +251,118 @@ func RegisterCommonFlags() {
 	// Randomize specs as well as suites
 	config.GinkgoConfig.RandomizeAllSpecs = true
 
-	flag.StringVar(&TestContext.GatherKubeSystemResourceUsageData, "gather-resource-usage", "false", "If set to 'true' or 'all' framework will be monitoring resource usage of system all add-ons in (some) e2e tests, if set to 'master' framework will be monitoring master node only, if set to 'none' of 'false' monitoring will be turned off.")
-	flag.BoolVar(&TestContext.GatherLogsSizes, "gather-logs-sizes", false, "If set to true framework will be monitoring logs sizes on all machines running e2e tests.")
-	flag.IntVar(&TestContext.MaxNodesToGather, "max-nodes-to-gather-from", 20, "The maximum number of nodes to gather extended info from on test failure.")
-	flag.StringVar(&TestContext.GatherMetricsAfterTest, "gather-metrics-at-teardown", "false", "If set to 'true' framework will gather metrics from all components after each test. If set to 'master' only master component metrics would be gathered.")
-	flag.BoolVar(&TestContext.GatherSuiteMetricsAfterTest, "gather-suite-metrics-at-teardown", false, "If set to true framwork will gather metrics from all components after the whole test suite completes.")
-	flag.BoolVar(&TestContext.AllowGatheringProfiles, "allow-gathering-profiles", true, "If set to true framework will allow to gather CPU/memory allocation pprof profiles from the master.")
-	flag.BoolVar(&TestContext.IncludeClusterAutoscalerMetrics, "include-cluster-autoscaler", false, "If set to true, framework will include Cluster Autoscaler when gathering metrics.")
-	flag.StringVar(&TestContext.OutputPrintType, "output-print-type", "json", "Format in which summaries should be printed: 'hr' for human readable, 'json' for JSON ones.")
-	flag.BoolVar(&TestContext.DumpLogsOnFailure, "dump-logs-on-failure", true, "If set to true test will dump data about the namespace in which test was running.")
-	flag.BoolVar(&TestContext.DisableLogDump, "disable-log-dump", false, "If set to true, logs from master and nodes won't be gathered after test run.")
-	flag.StringVar(&TestContext.LogexporterGCSPath, "logexporter-gcs-path", "", "Path to the GCS artifacts directory to dump logs from nodes. Logexporter gets enabled if this is non-empty.")
-	flag.BoolVar(&TestContext.DeleteNamespace, "delete-namespace", true, "If true tests will delete namespace after completion. It is only designed to make debugging easier, DO NOT turn it off by default.")
-	flag.BoolVar(&TestContext.DeleteNamespaceOnFailure, "delete-namespace-on-failure", true, "If true, framework will delete test namespace on failure. Used only during test debugging.")
-	flag.IntVar(&TestContext.AllowedNotReadyNodes, "allowed-not-ready-nodes", 0, "If non-zero, framework will allow for that many non-ready nodes when checking for all ready nodes.")
+	flags.StringVar(&TestContext.GatherKubeSystemResourceUsageData, "gather-resource-usage", "false", "If set to 'true' or 'all' framework will be monitoring resource usage of system all add-ons in (some) e2e tests, if set to 'master' framework will be monitoring master node only, if set to 'none' of 'false' monitoring will be turned off.")
+	flags.BoolVar(&TestContext.GatherLogsSizes, "gather-logs-sizes", false, "If set to true framework will be monitoring logs sizes on all machines running e2e tests.")
+	flags.IntVar(&TestContext.MaxNodesToGather, "max-nodes-to-gather-from", 20, "The maximum number of nodes to gather extended info from on test failure.")
+	flags.StringVar(&TestContext.GatherMetricsAfterTest, "gather-metrics-at-teardown", "false", "If set to 'true' framework will gather metrics from all components after each test. If set to 'master' only master component metrics would be gathered.")
+	flags.BoolVar(&TestContext.GatherSuiteMetricsAfterTest, "gather-suite-metrics-at-teardown", false, "If set to true framwork will gather metrics from all components after the whole test suite completes.")
+	flags.BoolVar(&TestContext.AllowGatheringProfiles, "allow-gathering-profiles", true, "If set to true framework will allow to gather CPU/memory allocation pprof profiles from the master.")
+	flags.BoolVar(&TestContext.IncludeClusterAutoscalerMetrics, "include-cluster-autoscaler", false, "If set to true, framework will include Cluster Autoscaler when gathering metrics.")
+	flags.StringVar(&TestContext.OutputPrintType, "output-print-type", "json", "Format in which summaries should be printed: 'hr' for human readable, 'json' for JSON ones.")
+	flags.BoolVar(&TestContext.DumpLogsOnFailure, "dump-logs-on-failure", true, "If set to true test will dump data about the namespace in which test was running.")
+	flags.BoolVar(&TestContext.DisableLogDump, "disable-log-dump", false, "If set to true, logs from master and nodes won't be gathered after test run.")
+	flags.StringVar(&TestContext.LogexporterGCSPath, "logexporter-gcs-path", "", "Path to the GCS artifacts directory to dump logs from nodes. Logexporter gets enabled if this is non-empty.")
+	flags.BoolVar(&TestContext.DeleteNamespace, "delete-namespace", true, "If true tests will delete namespace after completion. It is only designed to make debugging easier, DO NOT turn it off by default.")
+	flags.BoolVar(&TestContext.DeleteNamespaceOnFailure, "delete-namespace-on-failure", true, "If true, framework will delete test namespace on failure. Used only during test debugging.")
+	flags.IntVar(&TestContext.AllowedNotReadyNodes, "allowed-not-ready-nodes", 0, "If non-zero, framework will allow for that many non-ready nodes when checking for all ready nodes.")
 
-	flag.StringVar(&TestContext.Host, "host", "", fmt.Sprintf("The host, or apiserver, to connect to. Will default to %s if this argument and --kubeconfig are not set", defaultHost))
-	flag.StringVar(&TestContext.ReportPrefix, "report-prefix", "", "Optional prefix for JUnit XML reports. Default is empty, which doesn't prepend anything to the default name.")
-	flag.StringVar(&TestContext.ReportDir, "report-dir", "", "Path to the directory where the JUnit XML reports should be saved. Default is empty, which doesn't generate these reports.")
-	flag.Var(cliflag.NewMapStringBool(&TestContext.FeatureGates), "feature-gates", "A set of key=value pairs that describe feature gates for alpha/experimental features.")
-	flag.StringVar(&TestContext.ContainerRuntime, "container-runtime", "docker", "The container runtime of cluster VM instances (docker/remote).")
-	flag.StringVar(&TestContext.ContainerRuntimeEndpoint, "container-runtime-endpoint", "unix:///var/run/dockershim.sock", "The container runtime endpoint of cluster VM instances.")
-	flag.StringVar(&TestContext.ContainerRuntimeProcessName, "container-runtime-process-name", "dockerd", "The name of the container runtime process.")
-	flag.StringVar(&TestContext.ContainerRuntimePidFile, "container-runtime-pid-file", "/var/run/docker.pid", "The pid file of the container runtime.")
-	flag.StringVar(&TestContext.SystemdServices, "systemd-services", "docker", "The comma separated list of systemd services the framework will dump logs for.")
-	flag.BoolVar(&TestContext.DumpSystemdJournal, "dump-systemd-journal", false, "Whether to dump the full systemd journal.")
-	flag.StringVar(&TestContext.ImageServiceEndpoint, "image-service-endpoint", "", "The image service endpoint of cluster VM instances.")
-	flag.StringVar(&TestContext.DockershimCheckpointDir, "dockershim-checkpoint-dir", "/var/lib/dockershim/sandbox", "The directory for dockershim to store sandbox checkpoints.")
-	flag.StringVar(&TestContext.KubernetesAnywherePath, "kubernetes-anywhere-path", "/workspace/k8s.io/kubernetes-anywhere", "Which directory kubernetes-anywhere is installed to.")
+	flags.StringVar(&TestContext.Host, "host", "", fmt.Sprintf("The host, or apiserver, to connect to. Will default to %s if this argument and --kubeconfig are not set", defaultHost))
+	flags.StringVar(&TestContext.ReportPrefix, "report-prefix", "", "Optional prefix for JUnit XML reports. Default is empty, which doesn't prepend anything to the default name.")
+	flags.StringVar(&TestContext.ReportDir, "report-dir", "", "Path to the directory where the JUnit XML reports should be saved. Default is empty, which doesn't generate these reports.")
+	flags.Var(cliflag.NewMapStringBool(&TestContext.FeatureGates), "feature-gates", "A set of key=value pairs that describe feature gates for alpha/experimental features.")
+	flags.StringVar(&TestContext.ContainerRuntime, "container-runtime", "docker", "The container runtime of cluster VM instances (docker/remote).")
+	flags.StringVar(&TestContext.ContainerRuntimeEndpoint, "container-runtime-endpoint", "unix:///var/run/dockershim.sock", "The container runtime endpoint of cluster VM instances.")
+	flags.StringVar(&TestContext.ContainerRuntimeProcessName, "container-runtime-process-name", "dockerd", "The name of the container runtime process.")
+	flags.StringVar(&TestContext.ContainerRuntimePidFile, "container-runtime-pid-file", "/var/run/docker.pid", "The pid file of the container runtime.")
+	flags.StringVar(&TestContext.SystemdServices, "systemd-services", "docker", "The comma separated list of systemd services the framework will dump logs for.")
+	flags.BoolVar(&TestContext.DumpSystemdJournal, "dump-systemd-journal", false, "Whether to dump the full systemd journal.")
+	flags.StringVar(&TestContext.ImageServiceEndpoint, "image-service-endpoint", "", "The image service endpoint of cluster VM instances.")
+	flags.StringVar(&TestContext.DockershimCheckpointDir, "dockershim-checkpoint-dir", "/var/lib/dockershim/sandbox", "The directory for dockershim to store sandbox checkpoints.")
+	flags.StringVar(&TestContext.KubernetesAnywherePath, "kubernetes-anywhere-path", "/workspace/k8s.io/kubernetes-anywhere", "Which directory kubernetes-anywhere is installed to.")
 
-	flag.BoolVar(&TestContext.ListImages, "list-images", false, "If true, will show list of images used for runnning tests.")
+	flags.BoolVar(&TestContext.ListImages, "list-images", false, "If true, will show list of images used for runnning tests.")
 }
 
 // RegisterClusterFlags registers flags specific to the cluster e2e test suite.
-func RegisterClusterFlags() {
-	flag.BoolVar(&TestContext.VerifyServiceAccount, "e2e-verify-service-account", true, "If true tests will verify the service account before running.")
-	flag.StringVar(&TestContext.KubeConfig, clientcmd.RecommendedConfigPathFlag, os.Getenv(clientcmd.RecommendedConfigPathEnvVar), "Path to kubeconfig containing embedded authinfo.")
-	flag.StringVar(&TestContext.KubeContext, clientcmd.FlagContext, "", "kubeconfig context to use/override. If unset, will use value from 'current-context'")
-	flag.StringVar(&TestContext.KubeAPIContentType, "kube-api-content-type", "application/vnd.kubernetes.protobuf", "ContentType used to communicate with apiserver")
+func RegisterClusterFlags(flags *flag.FlagSet) {
+	flags.BoolVar(&TestContext.VerifyServiceAccount, "e2e-verify-service-account", true, "If true tests will verify the service account before running.")
+	flags.StringVar(&TestContext.KubeConfig, clientcmd.RecommendedConfigPathFlag, os.Getenv(clientcmd.RecommendedConfigPathEnvVar), "Path to kubeconfig containing embedded authinfo.")
+	flags.StringVar(&TestContext.KubeContext, clientcmd.FlagContext, "", "kubeconfig context to use/override. If unset, will use value from 'current-context'")
+	flags.StringVar(&TestContext.KubeAPIContentType, "kube-api-content-type", "application/vnd.kubernetes.protobuf", "ContentType used to communicate with apiserver")
 
-	flag.StringVar(&TestContext.KubeVolumeDir, "volume-dir", "/var/lib/kubelet", "Path to the directory containing the kubelet volumes.")
-	flag.StringVar(&TestContext.CertDir, "cert-dir", "", "Path to the directory containing the certs. Default is empty, which doesn't use certs.")
-	flag.StringVar(&TestContext.RepoRoot, "repo-root", "../../", "Root directory of kubernetes repository, for finding test files.")
-	flag.StringVar(&TestContext.Provider, "provider", "", "The name of the Kubernetes provider (gce, gke, local, skeleton (the fallback if not set), etc.)")
-	flag.StringVar(&TestContext.Tooling, "tooling", "", "The tooling in use (kops, gke, etc.)")
-	flag.StringVar(&TestContext.KubectlPath, "kubectl-path", "kubectl", "The kubectl binary to use. For development, you might use 'cluster/kubectl.sh' here.")
-	flag.StringVar(&TestContext.OutputDir, "e2e-output-dir", "/tmp", "Output directory for interesting/useful test data, like performance data, benchmarks, and other metrics.")
-	flag.StringVar(&TestContext.Prefix, "prefix", "e2e", "A prefix to be added to cloud resources created during testing.")
-	flag.StringVar(&TestContext.MasterOSDistro, "master-os-distro", "debian", "The OS distribution of cluster master (debian, ubuntu, gci, coreos, or custom).")
-	flag.StringVar(&TestContext.NodeOSDistro, "node-os-distro", "debian", "The OS distribution of cluster VM instances (debian, ubuntu, gci, coreos, or custom).")
-	flag.StringVar(&TestContext.ClusterMonitoringMode, "cluster-monitoring-mode", "standalone", "The monitoring solution that is used in the cluster.")
-	flag.BoolVar(&TestContext.EnablePrometheusMonitoring, "prometheus-monitoring", false, "Separate Prometheus monitoring deployed in cluster.")
-	flag.StringVar(&TestContext.ClusterDNSDomain, "dns-domain", "cluster.local", "The DNS Domain of the cluster.")
+	flags.StringVar(&TestContext.KubeVolumeDir, "volume-dir", "/var/lib/kubelet", "Path to the directory containing the kubelet volumes.")
+	flags.StringVar(&TestContext.CertDir, "cert-dir", "", "Path to the directory containing the certs. Default is empty, which doesn't use certs.")
+	flags.StringVar(&TestContext.RepoRoot, "repo-root", "../../", "Root directory of kubernetes repository, for finding test files.")
+	flags.StringVar(&TestContext.Provider, "provider", "", "The name of the Kubernetes provider (gce, gke, local, skeleton (the fallback if not set), etc.)")
+	flags.StringVar(&TestContext.Tooling, "tooling", "", "The tooling in use (kops, gke, etc.)")
+	flags.StringVar(&TestContext.KubectlPath, "kubectl-path", "kubectl", "The kubectl binary to use. For development, you might use 'cluster/kubectl.sh' here.")
+	flags.StringVar(&TestContext.OutputDir, "e2e-output-dir", "/tmp", "Output directory for interesting/useful test data, like performance data, benchmarks, and other metrics.")
+	flags.StringVar(&TestContext.Prefix, "prefix", "e2e", "A prefix to be added to cloud resources created during testing.")
+	flags.StringVar(&TestContext.MasterOSDistro, "master-os-distro", "debian", "The OS distribution of cluster master (debian, ubuntu, gci, coreos, or custom).")
+	flags.StringVar(&TestContext.NodeOSDistro, "node-os-distro", "debian", "The OS distribution of cluster VM instances (debian, ubuntu, gci, coreos, or custom).")
+	flags.StringVar(&TestContext.ClusterMonitoringMode, "cluster-monitoring-mode", "standalone", "The monitoring solution that is used in the cluster.")
+	flags.BoolVar(&TestContext.EnablePrometheusMonitoring, "prometheus-monitoring", false, "Separate Prometheus monitoring deployed in cluster.")
+	flags.StringVar(&TestContext.ClusterDNSDomain, "dns-domain", "cluster.local", "The DNS Domain of the cluster.")
 
 	// TODO: Flags per provider?  Rename gce-project/gce-zone?
 	cloudConfig := &TestContext.CloudConfig
-	flag.StringVar(&cloudConfig.MasterName, "kube-master", "", "Name of the kubernetes master. Only required if provider is gce or gke")
-	flag.StringVar(&cloudConfig.APIEndpoint, "gce-api-endpoint", "", "The GCE APIEndpoint being used, if applicable")
-	flag.StringVar(&cloudConfig.ProjectID, "gce-project", "", "The GCE project being used, if applicable")
-	flag.StringVar(&cloudConfig.Zone, "gce-zone", "", "GCE zone being used, if applicable")
-	flag.StringVar(&cloudConfig.Region, "gce-region", "", "GCE region being used, if applicable")
-	flag.BoolVar(&cloudConfig.MultiZone, "gce-multizone", false, "If true, start GCE cloud provider with multizone support.")
-	flag.BoolVar(&cloudConfig.MultiMaster, "gce-multimaster", false, "If true, the underlying GCE/GKE cluster is assumed to be multi-master.")
-	flag.StringVar(&cloudConfig.Cluster, "gke-cluster", "", "GKE name of cluster being used, if applicable")
-	flag.StringVar(&cloudConfig.NodeInstanceGroup, "node-instance-group", "", "Name of the managed instance group for nodes. Valid only for gce, gke or aws. If there is more than one group: comma separated list of groups.")
-	flag.StringVar(&cloudConfig.Network, "network", "e2e", "The cloud provider network for this e2e cluster.")
-	flag.IntVar(&cloudConfig.NumNodes, "num-nodes", DefaultNumNodes, fmt.Sprintf("Number of nodes in the cluster. If the default value of '%q' is used the number of schedulable nodes is auto-detected.", DefaultNumNodes))
-	flag.StringVar(&cloudConfig.ClusterIPRange, "cluster-ip-range", "10.64.0.0/14", "A CIDR notation IP range from which to assign IPs in the cluster.")
-	flag.StringVar(&cloudConfig.NodeTag, "node-tag", "", "Network tags used on node instances. Valid only for gce, gke")
-	flag.StringVar(&cloudConfig.MasterTag, "master-tag", "", "Network tags used on master instances. Valid only for gce, gke")
+	flags.StringVar(&cloudConfig.MasterName, "kube-master", "", "Name of the kubernetes master. Only required if provider is gce or gke")
+	flags.StringVar(&cloudConfig.APIEndpoint, "gce-api-endpoint", "", "The GCE APIEndpoint being used, if applicable")
+	flags.StringVar(&cloudConfig.ProjectID, "gce-project", "", "The GCE project being used, if applicable")
+	flags.StringVar(&cloudConfig.Zone, "gce-zone", "", "GCE zone being used, if applicable")
+	flags.StringVar(&cloudConfig.Region, "gce-region", "", "GCE region being used, if applicable")
+	flags.BoolVar(&cloudConfig.MultiZone, "gce-multizone", false, "If true, start GCE cloud provider with multizone support.")
+	flags.BoolVar(&cloudConfig.MultiMaster, "gce-multimaster", false, "If true, the underlying GCE/GKE cluster is assumed to be multi-master.")
+	flags.StringVar(&cloudConfig.Cluster, "gke-cluster", "", "GKE name of cluster being used, if applicable")
+	flags.StringVar(&cloudConfig.NodeInstanceGroup, "node-instance-group", "", "Name of the managed instance group for nodes. Valid only for gce, gke or aws. If there is more than one group: comma separated list of groups.")
+	flags.StringVar(&cloudConfig.Network, "network", "e2e", "The cloud provider network for this e2e cluster.")
+	flags.IntVar(&cloudConfig.NumNodes, "num-nodes", DefaultNumNodes, fmt.Sprintf("Number of nodes in the cluster. If the default value of '%q' is used the number of schedulable nodes is auto-detected.", DefaultNumNodes))
+	flags.StringVar(&cloudConfig.ClusterIPRange, "cluster-ip-range", "10.64.0.0/14", "A CIDR notation IP range from which to assign IPs in the cluster.")
+	flags.StringVar(&cloudConfig.NodeTag, "node-tag", "", "Network tags used on node instances. Valid only for gce, gke")
+	flags.StringVar(&cloudConfig.MasterTag, "master-tag", "", "Network tags used on master instances. Valid only for gce, gke")
 
-	flag.StringVar(&cloudConfig.ClusterTag, "cluster-tag", "", "Tag used to identify resources.  Only required if provider is aws.")
-	flag.StringVar(&cloudConfig.ConfigFile, "cloud-config-file", "", "Cloud config file.  Only required if provider is azure.")
-	flag.IntVar(&TestContext.MinStartupPods, "minStartupPods", 0, "The number of pods which we need to see in 'Running' state with a 'Ready' condition of true, before we try running tests. This is useful in any cluster which needs some base pod-based services running before it can be used.")
-	flag.DurationVar(&TestContext.SystemPodsStartupTimeout, "system-pods-startup-timeout", 10*time.Minute, "Timeout for waiting for all system pods to be running before starting tests.")
-	flag.DurationVar(&TestContext.NodeSchedulableTimeout, "node-schedulable-timeout", 30*time.Minute, "Timeout for waiting for all nodes to be schedulable.")
-	flag.DurationVar(&TestContext.SystemDaemonsetStartupTimeout, "system-daemonsets-startup-timeout", 5*time.Minute, "Timeout for waiting for all system daemonsets to be ready.")
-	flag.StringVar(&TestContext.EtcdUpgradeStorage, "etcd-upgrade-storage", "", "The storage version to upgrade to (either 'etcdv2' or 'etcdv3') if doing an etcd upgrade test.")
-	flag.StringVar(&TestContext.EtcdUpgradeVersion, "etcd-upgrade-version", "", "The etcd binary version to upgrade to (e.g., '3.0.14', '2.3.7') if doing an etcd upgrade test.")
-	flag.StringVar(&TestContext.GCEUpgradeScript, "gce-upgrade-script", "", "Script to use to upgrade a GCE cluster.")
-	flag.BoolVar(&TestContext.CleanStart, "clean-start", false, "If true, purge all namespaces except default and system before running tests. This serves to Cleanup test namespaces from failed/interrupted e2e runs in a long-lived cluster.")
+	flags.StringVar(&cloudConfig.ClusterTag, "cluster-tag", "", "Tag used to identify resources.  Only required if provider is aws.")
+	flags.StringVar(&cloudConfig.ConfigFile, "cloud-config-file", "", "Cloud config file.  Only required if provider is azure.")
+	flags.IntVar(&TestContext.MinStartupPods, "minStartupPods", 0, "The number of pods which we need to see in 'Running' state with a 'Ready' condition of true, before we try running tests. This is useful in any cluster which needs some base pod-based services running before it can be used.")
+	flags.DurationVar(&TestContext.SystemPodsStartupTimeout, "system-pods-startup-timeout", 10*time.Minute, "Timeout for waiting for all system pods to be running before starting tests.")
+	flags.DurationVar(&TestContext.NodeSchedulableTimeout, "node-schedulable-timeout", 30*time.Minute, "Timeout for waiting for all nodes to be schedulable.")
+	flags.DurationVar(&TestContext.SystemDaemonsetStartupTimeout, "system-daemonsets-startup-timeout", 5*time.Minute, "Timeout for waiting for all system daemonsets to be ready.")
+	flags.StringVar(&TestContext.EtcdUpgradeStorage, "etcd-upgrade-storage", "", "The storage version to upgrade to (either 'etcdv2' or 'etcdv3') if doing an etcd upgrade test.")
+	flags.StringVar(&TestContext.EtcdUpgradeVersion, "etcd-upgrade-version", "", "The etcd binary version to upgrade to (e.g., '3.0.14', '2.3.7') if doing an etcd upgrade test.")
+	flags.StringVar(&TestContext.GCEUpgradeScript, "gce-upgrade-script", "", "Script to use to upgrade a GCE cluster.")
+	flags.BoolVar(&TestContext.CleanStart, "clean-start", false, "If true, purge all namespaces except default and system before running tests. This serves to Cleanup test namespaces from failed/interrupted e2e runs in a long-lived cluster.")
 
 	nodeKiller := &TestContext.NodeKiller
-	flag.BoolVar(&nodeKiller.Enabled, "node-killer", false, "Whether NodeKiller should kill any nodes.")
-	flag.Float64Var(&nodeKiller.FailureRatio, "node-killer-failure-ratio", 0.01, "Percentage of nodes to be killed")
-	flag.DurationVar(&nodeKiller.Interval, "node-killer-interval", 1*time.Minute, "Time between node failures.")
-	flag.Float64Var(&nodeKiller.JitterFactor, "node-killer-jitter-factor", 60, "Factor used to jitter node failures.")
-	flag.DurationVar(&nodeKiller.SimulatedDowntime, "node-killer-simulated-downtime", 10*time.Minute, "A delay between node death and recreation")
+	flags.BoolVar(&nodeKiller.Enabled, "node-killer", false, "Whether NodeKiller should kill any nodes.")
+	flags.Float64Var(&nodeKiller.FailureRatio, "node-killer-failure-ratio", 0.01, "Percentage of nodes to be killed")
+	flags.DurationVar(&nodeKiller.Interval, "node-killer-interval", 1*time.Minute, "Time between node failures.")
+	flags.Float64Var(&nodeKiller.JitterFactor, "node-killer-jitter-factor", 60, "Factor used to jitter node failures.")
+	flags.DurationVar(&nodeKiller.SimulatedDowntime, "node-killer-simulated-downtime", 10*time.Minute, "A delay between node death and recreation")
 }
 
 // RegisterNodeFlags registers flags specific to the node e2e test suite.
-func RegisterNodeFlags() {
+func RegisterNodeFlags(flags *flag.FlagSet) {
 	// Mark the test as node e2e when node flags are api.Registry.
 	TestContext.NodeE2E = true
-	flag.StringVar(&TestContext.NodeName, "node-name", "", "Name of the node to run tests on.")
+	flags.StringVar(&TestContext.NodeName, "node-name", "", "Name of the node to run tests on.")
 	// TODO(random-liu): Move kubelet start logic out of the test.
 	// TODO(random-liu): Move log fetch logic out of the test.
 	// There are different ways to start kubelet (systemd, initd, docker, manually started etc.)
 	// and manage logs (journald, upstart etc.).
 	// For different situation we need to mount different things into the container, run different commands.
 	// It is hard and unnecessary to deal with the complexity inside the test suite.
-	flag.BoolVar(&TestContext.NodeConformance, "conformance", false, "If true, the test suite will not start kubelet, and fetch system log (kernel, docker, kubelet log etc.) to the report directory.")
-	flag.BoolVar(&TestContext.PrepullImages, "prepull-images", true, "If true, prepull images so image pull failures do not cause test failures.")
-	flag.StringVar(&TestContext.ImageDescription, "image-description", "", "The description of the image which the test will be running on.")
-	flag.StringVar(&TestContext.SystemSpecName, "system-spec-name", "", "The name of the system spec (e.g., gke) that's used in the node e2e test. The system specs are in test/e2e_node/system/specs/. This is used by the test framework to determine which tests to run for validating the system requirements.")
-	flag.Var(cliflag.NewMapStringString(&TestContext.ExtraEnvs), "extra-envs", "The extra environment variables needed for node e2e tests. Format: a list of key=value pairs, e.g., env1=val1,env2=val2")
+	flags.BoolVar(&TestContext.NodeConformance, "conformance", false, "If true, the test suite will not start kubelet, and fetch system log (kernel, docker, kubelet log etc.) to the report directory.")
+	flags.BoolVar(&TestContext.PrepullImages, "prepull-images", true, "If true, prepull images so image pull failures do not cause test failures.")
+	flags.StringVar(&TestContext.ImageDescription, "image-description", "", "The description of the image which the test will be running on.")
+	flags.StringVar(&TestContext.SystemSpecName, "system-spec-name", "", "The name of the system spec (e.g., gke) that's used in the node e2e test. The system specs are in test/e2e_node/system/specs/. This is used by the test framework to determine which tests to run for validating the system requirements.")
+	flags.Var(cliflag.NewMapStringString(&TestContext.ExtraEnvs), "extra-envs", "The extra environment variables needed for node e2e tests. Format: a list of key=value pairs, e.g., env1=val1,env2=val2")
 }
 
 // HandleFlags sets up all flags and parses the command line.
 func HandleFlags() {
-	RegisterCommonFlags()
-	RegisterClusterFlags()
+	e2econfig.CopyFlags(e2econfig.Flags, flag.CommandLine)
+	RegisterCommonFlags(flag.CommandLine)
+	RegisterClusterFlags(flag.CommandLine)
 	flag.Parse()
 }
 
diff --git a/test/e2e/framework/viperconfig/viperconfig.go b/test/e2e/framework/viperconfig/viperconfig.go
index 0b68174d2cf..b42ae73d9b3 100644
--- a/test/e2e/framework/viperconfig/viperconfig.go
+++ b/test/e2e/framework/viperconfig/viperconfig.go
@@ -25,8 +25,9 @@ import (
 	"github.com/spf13/viper"
 )
 
-// ViperizeFlags checks whether a configuration file was specified, reads it, and updates
-// the configuration variables accordingly. Must be called after framework.HandleFlags()
+// ViperizeFlags checks whether a configuration file was specified,
+// reads it, and updates the configuration variables in the specified
+// flag set accordingly. Must be called after framework.HandleFlags()
 // and before framework.AfterReadingAllFlags().
 //
 // The logic is so that a required configuration file must be present. If empty,
@@ -34,7 +35,7 @@ import (
 //
 // Files can be specified with just a base name ("e2e", matches "e2e.json/yaml/..." in
 // the current directory) or with path and suffix.
-func ViperizeFlags(requiredConfig, optionalConfig string) error {
+func ViperizeFlags(requiredConfig, optionalConfig string, flags *flag.FlagSet) error {
 	viperConfig := optionalConfig
 	required := false
 	if requiredConfig != "" {
@@ -99,24 +100,24 @@ func ViperizeFlags(requiredConfig, optionalConfig string) error {
 	// something like viper.Unmarshal(&TestContext) because we
 	// want to support all values, regardless where they are
 	// stored.
-	return wrapError(viperUnmarshal())
+	return wrapError(viperUnmarshal(flags))
 }
 
-// viperUnmarshall updates all command line flags with the corresponding values found
+// viperUnmarshall updates all flags with the corresponding values found
 // via Viper, regardless whether the flag value is stored in TestContext, some other
 // context or a local variable.
-func viperUnmarshal() error {
+func viperUnmarshal(flags *flag.FlagSet) error {
 	var result error
 	set := make(map[string]bool)
 
 	// Determine which values were already set explicitly via
 	// flags. Those we don't overwrite because command line
 	// flags have a higher priority.
-	flag.Visit(func(f *flag.Flag) {
+	flags.Visit(func(f *flag.Flag) {
 		set[f.Name] = true
 	})
 
-	flag.VisitAll(func(f *flag.Flag) {
+	flags.VisitAll(func(f *flag.Flag) {
 		if result != nil ||
 			set[f.Name] ||
 			!viper.IsSet(f.Name) {
diff --git a/test/e2e/framework/viperconfig/viperconfig_test.go b/test/e2e/framework/viperconfig/viperconfig_test.go
new file mode 100644
index 00000000000..7afa2bfe403
--- /dev/null
+++ b/test/e2e/framework/viperconfig/viperconfig_test.go
@@ -0,0 +1,72 @@
+/*
+Copyright 2019 The Kubernetes Authors.
+
+Licensed under the Apache License, Version 2.0 (the "License");
+you may not use this file except in compliance with the License.
+You may obtain a copy of the License at
+
+    http://www.apache.org/licenses/LICENSE-2.0
+
+Unless required by applicable law or agreed to in writing, software
+distributed under the License is distributed on an "AS IS" BASIS,
+WITHOUT WARRANTIES OR CONDITIONS OF ANY KIND, either express or implied.
+See the License for the specific language governing permissions and
+limitations under the License.
+*/
+
+package viperconfig
+
+import (
+	"flag"
+	"io/ioutil"
+	"os"
+	"testing"
+	"time"
+
+	"github.com/stretchr/testify/require"
+	"k8s.io/kubernetes/test/e2e/framework/config"
+)
+
+func TestViperConfig(t *testing.T) {
+	flags := flag.NewFlagSet("test", 0)
+	type Context struct {
+		Bool     bool          `default:"true"`
+		Duration time.Duration `default:"1ms"`
+		Float64  float64       `default:"1.23456789"`
+		String   string        `default:"hello world"`
+		Int      int           `default:"-1" usage:"some number"`
+		Int64    int64         `default:"-1234567890123456789"`
+		Uint     uint          `default:"1"`
+		Uint64   uint64        `default:"1234567890123456789"`
+	}
+	var context Context
+	require.NotPanics(t, func() {
+		config.AddOptionsToSet(flags, &context, "")
+	})
+
+	config := `
+bool: false
+duration: 1s
+float64: -1.23456789
+string: pong
+int: -2
+int64: -9123456789012345678
+uint: 2
+uint64: 9123456789012345678
+`
+	tmpfile, err := ioutil.TempFile("", "viperconfig-*.yaml")
+	require.NoError(t, err, "temp file")
+	defer os.Remove(tmpfile.Name())
+	if _, err := tmpfile.Write([]byte(config)); err != nil {
+		require.NoError(t, err, "write config")
+	}
+	require.NoError(t, tmpfile.Close(), "close temp file")
+
+	require.NoError(t, ViperizeFlags(tmpfile.Name(), "", flags), "read config file")
+	require.Equal(t,
+		Context{false, time.Second, -1.23456789, "pong",
+			-2, -9123456789012345678, 2, 9123456789012345678,
+		},
+		context,
+		"values from viper must match")
+}
diff --git a/test/e2e/lifecycle/cluster_upgrade.go b/test/e2e/lifecycle/cluster_upgrade.go
index ee5dc3929ba..29dafd741d7 100644
--- a/test/e2e/lifecycle/cluster_upgrade.go
+++ b/test/e2e/lifecycle/cluster_upgrade.go
@@ -18,7 +18,6 @@ package lifecycle
 
 import (
 	"encoding/xml"
-	"flag"
 	"fmt"
 	"os"
 	"path/filepath"
@@ -31,6 +30,7 @@ import (
 	"k8s.io/client-go/discovery"
 	"k8s.io/kubernetes/test/e2e/chaosmonkey"
 	"k8s.io/kubernetes/test/e2e/framework"
+	"k8s.io/kubernetes/test/e2e/framework/config"
 	"k8s.io/kubernetes/test/e2e/framework/ginkgowrapper"
 	e2elifecycle "k8s.io/kubernetes/test/e2e/framework/lifecycle"
 	"k8s.io/kubernetes/test/e2e/upgrades"
@@ -42,8 +42,8 @@ import (
 )
 
 var (
-	upgradeTarget = flag.String("upgrade-target", "ci/latest", "Version to upgrade to (e.g. 'release/stable', 'release/latest', 'ci/latest', '0.19.1', '0.19.1-669-gabac8c8') if doing an upgrade test.")
-	upgradeImage  = flag.String("upgrade-image", "", "Image to upgrade to (e.g. 'container_vm' or 'gci') if doing an upgrade test.")
+	upgradeTarget = config.Flags.String("upgrade-target", "ci/latest", "Version to upgrade to (e.g. 'release/stable', 'release/latest', 'ci/latest', '0.19.1', '0.19.1-669-gabac8c8') if doing an upgrade test.")
+	upgradeImage  = config.Flags.String("upgrade-image", "", "Image to upgrade to (e.g. 'container_vm' or 'gci') if doing an upgrade test.")
 )
 
 var upgradeTests = []upgrades.Test{
diff --git a/test/e2e/storage/drivers/csi.go b/test/e2e/storage/drivers/csi.go
index 06b57b4dfec..e7a0dbb669d 100644
--- a/test/e2e/storage/drivers/csi.go
+++ b/test/e2e/storage/drivers/csi.go
@@ -144,8 +144,6 @@ func (h *hostpathCSIDriver) PrepareTest(f *framework.Framework) (*testsuites.Per
 		ClientNodeName: nodeName,
 	}
 
-	// TODO (?): the storage.csi.image.version and storage.csi.image.registry
-	// settings are ignored for this test. We could patch the image definitions.
 	o := utils.PatchCSIOptions{
 		OldDriverName:            h.driverInfo.Name,
 		NewDriverName:            config.GetUniqueDriverName(),
@@ -288,8 +286,6 @@ func (m *mockCSIDriver) PrepareTest(f *framework.Framework) (*testsuites.PerTest
 		containerArgs = append(containerArgs, "--node-expand-required=true")
 	}
 
-	// TODO (?): the storage.csi.image.version and storage.csi.image.registry
-	// settings are ignored for this test. We could patch the image definitions.
 	o := utils.PatchCSIOptions{
 		OldDriverName:                 "csi-mock",
 		NewDriverName:                 "csi-mock-" + f.UniqueName,
diff --git a/test/e2e/storage/external/external.go b/test/e2e/storage/external/external.go
index 3b712dd252a..616c6433638 100644
--- a/test/e2e/storage/external/external.go
+++ b/test/e2e/storage/external/external.go
@@ -30,6 +30,7 @@ import (
 	"k8s.io/apiserver/pkg/storage/names"
 	"k8s.io/client-go/kubernetes/scheme"
 	"k8s.io/kubernetes/test/e2e/framework"
+	"k8s.io/kubernetes/test/e2e/framework/config"
 	"k8s.io/kubernetes/test/e2e/storage/testpatterns"
 	"k8s.io/kubernetes/test/e2e/storage/testsuites"
 
@@ -49,7 +50,7 @@ var csiTestSuites = []func() testsuites.TestSuite{
 }
 
 func init() {
-	flag.Var(testDriverParameter{}, "storage.testdriver", "name of a .yaml or .json file that defines a driver for storage testing, can be used more than once")
+	config.Flags.Var(testDriverParameter{}, "storage.testdriver", "name of a .yaml or .json file that defines a driver for storage testing, can be used more than once")
 }
 
 // testDriverParameter is used to hook loading of the driver
diff --git a/test/e2e/storage/utils/deployment.go b/test/e2e/storage/utils/deployment.go
index c14ba2f7976..b1a3aed5af5 100644
--- a/test/e2e/storage/utils/deployment.go
+++ b/test/e2e/storage/utils/deployment.go
@@ -49,10 +49,6 @@ import (
 //
 // Driver deployments that are different will have to do the patching
 // without this function, or skip patching entirely.
-//
-// TODO (?): the storage.csi.image.version and storage.csi.image.registry
-// settings are ignored. We could patch the image definitions or deprecate
-// those options.
 func PatchCSIDeployment(f *framework.Framework, o PatchCSIOptions, object interface{}) error {
 	rename := o.OldDriverName != "" && o.NewDriverName != "" &&
 		o.OldDriverName != o.NewDriverName
diff --git a/test/e2e_kubeadm/e2e_kubeadm_suite_test.go b/test/e2e_kubeadm/e2e_kubeadm_suite_test.go
index 6d1817bbca4..9a508138f94 100644
--- a/test/e2e_kubeadm/e2e_kubeadm_suite_test.go
+++ b/test/e2e_kubeadm/e2e_kubeadm_suite_test.go
@@ -30,11 +30,13 @@ import (
 
 	morereporters "github.com/onsi/ginkgo/reporters"
 	"k8s.io/kubernetes/test/e2e/framework"
+	e2econfig "k8s.io/kubernetes/test/e2e/framework/config"
 )
 
 func init() {
-	framework.RegisterCommonFlags()
-	framework.RegisterClusterFlags()
+	e2econfig.CopyFlags(e2econfig.Flags, flag.CommandLine)
+	framework.RegisterCommonFlags(flag.CommandLine)
+	framework.RegisterClusterFlags(flag.CommandLine)
 
 	pflag.CommandLine.AddGoFlagSet(flag.CommandLine)
 }
diff --git a/test/e2e_node/e2e_node_suite_test.go b/test/e2e_node/e2e_node_suite_test.go
index bf920672ba2..409d5286f0d 100644
--- a/test/e2e_node/e2e_node_suite_test.go
+++ b/test/e2e_node/e2e_node_suite_test.go
@@ -41,6 +41,7 @@ import (
 	"k8s.io/kubernetes/cmd/kubeadm/app/util/system"
 	commontest "k8s.io/kubernetes/test/e2e/common"
 	"k8s.io/kubernetes/test/e2e/framework"
+	e2econfig "k8s.io/kubernetes/test/e2e/framework/config"
 	"k8s.io/kubernetes/test/e2e/framework/testfiles"
 	"k8s.io/kubernetes/test/e2e/generated"
 	"k8s.io/kubernetes/test/e2e_node/services"
@@ -63,8 +64,9 @@ var systemValidateMode = flag.Bool("system-validate-mode", false, "If true, only
 var systemSpecFile = flag.String("system-spec-file", "", "The name of the system spec file that will be used for node conformance test. If it's unspecified or empty, the default system spec (system.DefaultSysSpec) will be used.")
 
 func init() {
-	framework.RegisterCommonFlags()
-	framework.RegisterNodeFlags()
+	e2econfig.CopyFlags(e2econfig.Flags, flag.CommandLine)
+	framework.RegisterCommonFlags(flag.CommandLine)
+	framework.RegisterNodeFlags(flag.CommandLine)
 	pflag.CommandLine.AddGoFlagSet(flag.CommandLine)
 	// Mark the run-services-mode flag as hidden to prevent user from using it.
 	pflag.CommandLine.MarkHidden("run-services-mode")