diff --git a/cmd/kube-scheduler/app/options/deprecated.go b/cmd/kube-scheduler/app/options/deprecated.go
index bae856bbde7..089c510f825 100644
--- a/cmd/kube-scheduler/app/options/deprecated.go
+++ b/cmd/kube-scheduler/app/options/deprecated.go
@@ -47,12 +47,12 @@ func (o *DeprecatedOptions) AddFlags(fs *pflag.FlagSet, cfg *kubeschedulerconfig
 		return
 	}
 
-	fs.StringVar(&o.AlgorithmProvider, "algorithm-provider", o.AlgorithmProvider, "DEPRECATED: the scheduling algorithm provider to use, one of: "+algorithmprovider.ListAlgorithmProviders())
-	fs.StringVar(&o.PolicyConfigFile, "policy-config-file", o.PolicyConfigFile, "DEPRECATED: file with scheduler policy configuration. This file is used if policy ConfigMap is not provided or --use-legacy-policy-config=true")
-	usage := fmt.Sprintf("DEPRECATED: name of the ConfigMap object that contains scheduler's policy configuration. It must exist in the system namespace before scheduler initialization if --use-legacy-policy-config=false. The config must be provided as the value of an element in 'Data' map with the key='%v'", kubeschedulerconfig.SchedulerPolicyConfigMapKey)
+	fs.StringVar(&o.AlgorithmProvider, "algorithm-provider", o.AlgorithmProvider, "DEPRECATED: the scheduling algorithm provider to use, this sets the default plugins for component config profiles. Choose one of: "+algorithmprovider.ListAlgorithmProviders())
+	fs.StringVar(&o.PolicyConfigFile, "policy-config-file", o.PolicyConfigFile, "DEPRECATED: file with scheduler policy configuration. This file is used if policy ConfigMap is not provided or --use-legacy-policy-config=true. Note: The scheduler will fail if this is combined with Plugin configs")
+	usage := fmt.Sprintf("DEPRECATED: name of the ConfigMap object that contains scheduler's policy configuration. It must exist in the system namespace before scheduler initialization if --use-legacy-policy-config=false. The config must be provided as the value of an element in 'Data' map with the key='%v'. Note: The scheduler will fail if this is combined with Plugin configs", kubeschedulerconfig.SchedulerPolicyConfigMapKey)
 	fs.StringVar(&o.PolicyConfigMapName, "policy-configmap", o.PolicyConfigMapName, usage)
-	fs.StringVar(&o.PolicyConfigMapNamespace, "policy-configmap-namespace", o.PolicyConfigMapNamespace, "DEPRECATED: the namespace where policy ConfigMap is located. The kube-system namespace will be used if this is not provided or is empty.")
-	fs.BoolVar(&o.UseLegacyPolicyConfig, "use-legacy-policy-config", o.UseLegacyPolicyConfig, "DEPRECATED: when set to true, scheduler will ignore policy ConfigMap and uses policy config file")
+	fs.StringVar(&o.PolicyConfigMapNamespace, "policy-configmap-namespace", o.PolicyConfigMapNamespace, "DEPRECATED: the namespace where policy ConfigMap is located. The kube-system namespace will be used if this is not provided or is empty. Note: The scheduler will fail if this is combined with Plugin configs")
+	fs.BoolVar(&o.UseLegacyPolicyConfig, "use-legacy-policy-config", o.UseLegacyPolicyConfig, "DEPRECATED: when set to true, scheduler will ignore policy ConfigMap and uses policy config file. Note: The scheduler will fail if this is combined with Plugin configs")
 
 	fs.BoolVar(&cfg.EnableProfiling, "profiling", cfg.EnableProfiling, "DEPRECATED: enable profiling via web interface host:port/debug/pprof/")
 	fs.BoolVar(&cfg.EnableContentionProfiling, "contention-profiling", cfg.EnableContentionProfiling, "DEPRECATED: enable lock contention profiling, if profiling is enabled")
@@ -87,16 +87,14 @@ func (o *DeprecatedOptions) Validate() []error {
 	return errs
 }
 
-// ApplyTo sets cfg.AlgorithmSource from flags passed on the command line in the following precedence order:
+// ApplyAlgorithmSourceTo sets cfg.AlgorithmSource from flags passed on the command line in the following precedence order:
 //
 // 1. --use-legacy-policy-config to use a policy file.
 // 2. --policy-configmap to use a policy config map value.
 // 3. --algorithm-provider to use a named algorithm provider.
-//
-// This function is only called when no config file is provided.
-func (o *DeprecatedOptions) ApplyTo(cfg *kubeschedulerconfig.KubeSchedulerConfiguration) error {
+func (o *DeprecatedOptions) ApplyAlgorithmSourceTo(cfg *kubeschedulerconfig.KubeSchedulerConfiguration) {
 	if o == nil {
-		return nil
+		return
 	}
 
 	switch {
@@ -122,10 +120,19 @@ func (o *DeprecatedOptions) ApplyTo(cfg *kubeschedulerconfig.KubeSchedulerConfig
 			Provider: &o.AlgorithmProvider,
 		}
 	}
+}
 
-	// Deprecated flags have an effect iff no config file was provided, in which
-	// case this function expects a default KubeSchedulerConfiguration instance,
-	// which has a single profile.
+// ApplyTo sets a default profile plugin config if no config file is specified
+// It also calls ApplyAlgorithmSourceTo to set Policy settings in AlgorithmSource, if applicable.
+// Deprecated flags have an effect iff no config file was provided, in which
+// case this function expects a default KubeSchedulerConfiguration instance,
+// which has a single profile.
+func (o *DeprecatedOptions) ApplyTo(cfg *kubeschedulerconfig.KubeSchedulerConfiguration) {
+	if o == nil {
+		return
+	}
+	// The following deprecated options affect the only existing profile that is
+	// added by default.
 	profile := &cfg.Profiles[0]
 	if len(o.SchedulerName) > 0 {
 		profile.SchedulerName = o.SchedulerName
@@ -136,6 +143,7 @@ func (o *DeprecatedOptions) ApplyTo(cfg *kubeschedulerconfig.KubeSchedulerConfig
 			HardPodAffinityWeight: o.HardPodAffinitySymmetricWeight,
 		},
 	}
+
 	profile.PluginConfig = append(profile.PluginConfig, plCfg)
-	return nil
+	o.ApplyAlgorithmSourceTo(cfg)
 }
diff --git a/cmd/kube-scheduler/app/options/options.go b/cmd/kube-scheduler/app/options/options.go
index 7dc1d31d0e4..465f30fdb82 100644
--- a/cmd/kube-scheduler/app/options/options.go
+++ b/cmd/kube-scheduler/app/options/options.go
@@ -148,7 +148,13 @@ func newDefaultComponentConfig() (*kubeschedulerconfig.KubeSchedulerConfiguratio
 // Flags returns flags for a specific scheduler by section name
 func (o *Options) Flags() (nfs cliflag.NamedFlagSets) {
 	fs := nfs.FlagSet("misc")
-	fs.StringVar(&o.ConfigFile, "config", o.ConfigFile, "The path to the configuration file. Flags override values in this file.")
+	fs.StringVar(&o.ConfigFile, "config", o.ConfigFile, `The path to the configuration file. The following flags can overwrite fields in this file:
+  --address
+  --port
+  --use-legacy-policy-config
+  --policy-configmap
+  --policy-config-file
+  --algorithm-provider`)
 	fs.StringVar(&o.WriteConfigTo, "write-config-to", o.WriteConfigTo, "If set, write the configuration values to this file and exit.")
 	fs.StringVar(&o.Master, "master", o.Master, "The address of the Kubernetes API server (overrides any value in kubeconfig)")
 
@@ -170,10 +176,8 @@ func (o *Options) ApplyTo(c *schedulerappconfig.Config) error {
 	if len(o.ConfigFile) == 0 {
 		c.ComponentConfig = o.ComponentConfig
 
-		// only apply deprecated flags if no config file is loaded (this is the old behaviour).
-		if err := o.Deprecated.ApplyTo(&c.ComponentConfig); err != nil {
-			return err
-		}
+		// apply deprecated flags if no config file is loaded (this is the old behaviour).
+		o.Deprecated.ApplyTo(&c.ComponentConfig)
 		if err := o.CombinedInsecureServing.ApplyTo(c, &c.ComponentConfig); err != nil {
 			return err
 		}
@@ -186,11 +190,18 @@ func (o *Options) ApplyTo(c *schedulerappconfig.Config) error {
 			return err
 		}
 
-		// use the loaded config file only, with the exception of --address and --port. This means that
-		// none of the deprecated flags in o.Deprecated are taken into consideration. This is the old
-		// behaviour of the flags we have to keep.
 		c.ComponentConfig = *cfg
 
+		// apply any deprecated Policy flags, if applicable
+		o.Deprecated.ApplyAlgorithmSourceTo(&c.ComponentConfig)
+
+		// if the user has set CC profiles and is trying to use a Policy config, error out
+		// these configs are no longer merged and they should not be used simultaneously
+		if !emptySchedulerProfileConfig(c.ComponentConfig.Profiles) && c.ComponentConfig.AlgorithmSource.Policy != nil {
+			return fmt.Errorf("cannot set a Plugin config and Policy config")
+		}
+
+		// use the loaded config file only, with the exception of --address and --port.
 		if err := o.CombinedInsecureServing.ApplyToFromLoadedConfig(c, &c.ComponentConfig); err != nil {
 			return err
 		}
@@ -211,6 +222,15 @@ func (o *Options) ApplyTo(c *schedulerappconfig.Config) error {
 	return nil
 }
 
+// emptySchedulerProfileConfig returns true if the list of profiles passed to it contains only
+// the "default-scheduler" profile with no plugins or pluginconfigs registered
+// (this is the default empty profile initialized by defaults.go)
+func emptySchedulerProfileConfig(profiles []kubeschedulerconfig.KubeSchedulerProfile) bool {
+	return len(profiles) == 1 &&
+		len(profiles[0].PluginConfig) == 0 &&
+		profiles[0].Plugins == nil
+}
+
 // Validate validates all the required options.
 func (o *Options) Validate() []error {
 	var errs []error
diff --git a/cmd/kube-scheduler/app/options/options_test.go b/cmd/kube-scheduler/app/options/options_test.go
index ad300ef3e64..4d463cb2a0c 100644
--- a/cmd/kube-scheduler/app/options/options_test.go
+++ b/cmd/kube-scheduler/app/options/options_test.go
@@ -721,6 +721,16 @@ profiles:
 				},
 			},
 		},
+		{
+			name: "Attempting to set Component Config Profiles and Policy config",
+			options: &Options{
+				ConfigFile: pluginConfigFile,
+				Deprecated: &DeprecatedOptions{
+					PolicyConfigMapName: "bar",
+				},
+			},
+			expectedError: "cannot set a Plugin config and Policy config",
+		},
 		{
 			name: "unknown field",
 			options: &Options{