diff --git a/internal/agent/install_test.go b/internal/agent/install_test.go
index a7321f6..b5fdd79 100644
--- a/internal/agent/install_test.go
+++ b/internal/agent/install_test.go
@@ -3,13 +3,14 @@ package agent
 import (
 	"context"
 	"fmt"
-	"github.com/jaypipes/ghw/pkg/block"
-	"github.com/kairos-io/kairos-agent/v2/pkg/constants"
 	"os"
 	"path/filepath"
 
+	"github.com/jaypipes/ghw/pkg/block"
+	"github.com/kairos-io/kairos-agent/v2/pkg/constants"
+
 	"github.com/kairos-io/kairos-agent/v2/pkg/config"
-	"github.com/kairos-io/kairos-agent/v2/pkg/utils/fs"
+	fsutils "github.com/kairos-io/kairos-agent/v2/pkg/utils/fs"
 	v1mock "github.com/kairos-io/kairos-agent/v2/tests/mocks"
 	"github.com/twpayne/go-vfs"
 	"github.com/twpayne/go-vfs/vfst"
@@ -196,7 +197,7 @@ var _ = Describe("RunInstall", func() {
 
 	It("runs the install", func() {
 		Skip("Not ready yet")
-		err = RunInstall(options)
+		err = RunInstall(options, "") // TODO
 		Expect(err).ToNot(HaveOccurred())
 	})
 })
diff --git a/internal/agent/upgrade.go b/internal/agent/upgrade.go
index 4c6d5db..7c0907a 100644
--- a/internal/agent/upgrade.go
+++ b/internal/agent/upgrade.go
@@ -60,6 +60,11 @@ func Upgrade(
 		return err
 	}
 
+	err = upgradeSpec.Sanitize()
+	if err != nil {
+		return err
+	}
+
 	upgradeAction := action.NewUpgradeAction(c, upgradeSpec)
 
 	err = upgradeAction.Run()
@@ -105,9 +110,9 @@ func determineUpgradeImage(version string) (*v1.ImageSource, error) {
 	return v1.NewSrcFromURI(fmt.Sprintf("%s:%s", registry, version))
 }
 
-// generateUpgradeConf creates a kairos configuration for `--source` and `--recovery`
+// generateConfForCLIArgs creates a kairos configuration for `--source` and `--recovery`
 // command line arguments. It will be added to the rest of the configurations.
-func generateUpgradeConf(source string, upgradeRecovery bool) (string, error) {
+func generateConfForCLIArgs(source string, upgradeRecovery bool) (string, error) {
 	upgrade := map[string](map[string]interface{}){
 		"upgrade": {},
 	}
@@ -193,13 +198,13 @@ func findLatestVersion(preReleases, force bool) (string, error) {
 }
 
 func generateUpgradeSpec(version, source string, force, strictValidations bool, dirs []string, preReleases, upgradeRecovery bool) (*v1.UpgradeSpec, *config.Config, error) {
-	upgradeConf, err := generateUpgradeConf(source, upgradeRecovery)
+	cliConf, err := generateConfForCLIArgs(source, upgradeRecovery)
 	if err != nil {
 		return nil, nil, err
 	}
 
 	c, err := config.Scan(collector.Directories(dirs...),
-		collector.Readers(strings.NewReader(upgradeConf)),
+		collector.Readers(strings.NewReader(cliConf)),
 		collector.StrictValidation(strictValidations))
 	if err != nil {
 		return nil, nil, err
@@ -218,11 +223,5 @@ func generateUpgradeSpec(version, source string, force, strictValidations bool,
 		return nil, nil, err
 	}
 
-	// Sanitize
-	err = upgradeSpec.Sanitize()
-	if err != nil {
-		return nil, nil, err
-	}
-
 	return upgradeSpec, c, nil
 }
diff --git a/internal/agent/upgrade_test.go b/internal/agent/upgrade_test.go
new file mode 100644
index 0000000..ffa4da8
--- /dev/null
+++ b/internal/agent/upgrade_test.go
@@ -0,0 +1,47 @@
+package agent
+
+import (
+	"fmt"
+	"os"
+	"path"
+
+	. "github.com/onsi/ginkgo/v2"
+	. "github.com/onsi/gomega"
+)
+
+var _ = Describe("generateUpgradeSpec", func() {
+	When("there are command line arguments", func() {
+		var configDir string
+		var upgradeRecovery bool
+
+		BeforeEach(func() {
+			upgradeRecovery = false
+			configDir, err := os.MkdirTemp("", "upgrade-test")
+			Expect(err).ToNot(HaveOccurred())
+
+			config := fmt.Sprintf(`upgrade:
+  recovery: %t
+  recovery-system:
+    uri: oci://image-in-conf
+`, upgradeRecovery)
+
+			configFilePath := path.Join(configDir, "config.yaml")
+			err = os.WriteFile(configFilePath, []byte(config), os.ModePerm)
+			Expect(err).ToNot(HaveOccurred())
+		})
+
+		AfterEach(func() {
+			os.RemoveAll(configDir)
+		})
+
+		It("overrides kairos config yaml values", func() {
+			spec, _, err := generateUpgradeSpec("", "oci:myimage", false, false,
+				[]string{}, false, !upgradeRecovery)
+
+			Expect(err).ToNot(HaveOccurred())
+			Expect(spec.Active.Source.String()).To(Equal("oci://myimage:latest"))
+			Expect(spec.Recovery.Source.String()).To(Equal("oci://myimage:latest"))
+			Expect(spec.RecoveryUpgrade).To(Equal(!upgradeRecovery))
+		})
+	})
+})
diff --git a/pkg/config/spec.go b/pkg/config/spec.go
index cda731d..261c723 100644
--- a/pkg/config/spec.go
+++ b/pkg/config/spec.go
@@ -544,8 +544,6 @@ func ReadUpgradeSpecFromConfig(c *Config) (*v1.UpgradeSpec, error) {
 
 // ReadSpecFromCloudConfig returns a v1.Spec for the given spec
 func ReadSpecFromCloudConfig(r *Config, spec string) (v1.Spec, error) {
-	fmt.Printf("litter.Sdump(r) before = %+v\n", litter.Sdump(r))
-
 	var sp v1.Spec
 	var err error
 
@@ -563,8 +561,6 @@ func ReadSpecFromCloudConfig(r *Config, spec string) (v1.Spec, error) {
 		return nil, fmt.Errorf("failed initializing spec: %v", err)
 	}
 
-	fmt.Printf("litter.Sdump(sp) before = %+v\n", litter.Sdump(sp))
-
 	// Load the config into viper from the raw cloud config string
 	ccString, err := r.String()
 	if err != nil {
@@ -582,10 +578,6 @@ func ReadSpecFromCloudConfig(r *Config, spec string) (v1.Spec, error) {
 		r.Logger.Warnf("error unmarshalling %s Spec: %s", spec, err)
 	}
 
-	fmt.Println("---------------------------------")
-	fmt.Printf("litter.Sdump(sp) after = %+v\n", litter.Sdump(sp))
-	fmt.Println("---------------------------------")
-
 	r.Logger.Debugf("Loaded %s spec: %s", spec, litter.Sdump(sp))
 	return sp, nil
 }