diff --git a/pkg/commands/clean/run.go b/pkg/commands/clean/run.go
index c60227360d19..8dd83519422f 100644
--- a/pkg/commands/clean/run.go
+++ b/pkg/commands/clean/run.go
@@ -2,7 +2,6 @@ package clean
 
 import (
 	"context"
-	"os"
 
 	"golang.org/x/xerrors"
 
@@ -25,7 +24,11 @@ func Run(ctx context.Context, opts flag.Options) error {
 	}
 
 	if opts.CleanAll {
-		return cleanAll(ctx, opts)
+		opts.CleanScanCache = true
+		opts.CleanVulnerabilityDB = true
+		opts.CleanJavaDB = true
+		opts.CleanChecksBundle = true
+		opts.CleanVEXRepositories = true
 	}
 
 	if opts.CleanScanCache {
@@ -60,14 +63,6 @@ func Run(ctx context.Context, opts flag.Options) error {
 	return nil
 }
 
-func cleanAll(ctx context.Context, opts flag.Options) error {
-	log.InfoContext(ctx, "Removing all caches...")
-	if err := os.RemoveAll(opts.CacheDir); err != nil {
-		return xerrors.Errorf("failed to remove the directory (%s) : %w", opts.CacheDir, err)
-	}
-	return nil
-}
-
 func cleanScanCache(ctx context.Context, opts flag.Options) error {
 	log.InfoContext(ctx, "Removing scan cache...")
 	c, cleanup, err := cache.New(opts.CacheOpts())
diff --git a/pkg/commands/clean/run_test.go b/pkg/commands/clean/run_test.go
index 9b301d238219..32e4110aba97 100644
--- a/pkg/commands/clean/run_test.go
+++ b/pkg/commands/clean/run_test.go
@@ -28,7 +28,12 @@ func TestRun(t *testing.T) {
 			},
 			wantErr: false,
 			checkFunc: func(t *testing.T, dir string) {
-				assert.NoDirExists(t, dir)
+				assert.NoDirExists(t, filepath.Join(dir, "fanal"))
+				assert.NoDirExists(t, filepath.Join(dir, "db"))
+				assert.NoDirExists(t, filepath.Join(dir, "java-db"))
+				assert.NoDirExists(t, filepath.Join(dir, "policy"))
+				assert.NoDirExists(t, filepath.Join(dir, "vex"))
+				assert.DirExists(t, dir)
 			},
 		},
 		{
@@ -42,6 +47,7 @@ func TestRun(t *testing.T) {
 				assert.DirExists(t, filepath.Join(dir, "db"))
 				assert.DirExists(t, filepath.Join(dir, "java-db"))
 				assert.DirExists(t, filepath.Join(dir, "policy"))
+				assert.DirExists(t, filepath.Join(dir, "vex"))
 			},
 		},
 		{
@@ -55,6 +61,7 @@ func TestRun(t *testing.T) {
 				assert.DirExists(t, filepath.Join(dir, "fanal"))
 				assert.DirExists(t, filepath.Join(dir, "java-db"))
 				assert.DirExists(t, filepath.Join(dir, "policy"))
+				assert.DirExists(t, filepath.Join(dir, "vex"))
 			},
 		},
 		{
@@ -68,6 +75,7 @@ func TestRun(t *testing.T) {
 				assert.DirExists(t, filepath.Join(dir, "fanal"))
 				assert.DirExists(t, filepath.Join(dir, "db"))
 				assert.DirExists(t, filepath.Join(dir, "policy"))
+				assert.DirExists(t, filepath.Join(dir, "vex"))
 			},
 		},
 		{
@@ -81,6 +89,21 @@ func TestRun(t *testing.T) {
 				assert.DirExists(t, filepath.Join(dir, "fanal"))
 				assert.DirExists(t, filepath.Join(dir, "db"))
 				assert.DirExists(t, filepath.Join(dir, "java-db"))
+				assert.DirExists(t, filepath.Join(dir, "vex"))
+			},
+		},
+		{
+			name: "clean vex repositories",
+			cleanOpts: flag.CleanOptions{
+				CleanVEXRepositories: true,
+			},
+			wantErr: false,
+			checkFunc: func(t *testing.T, dir string) {
+				assert.DirExists(t, filepath.Join(dir, "policy"))
+				assert.DirExists(t, filepath.Join(dir, "fanal"))
+				assert.DirExists(t, filepath.Join(dir, "db"))
+				assert.DirExists(t, filepath.Join(dir, "java-db"))
+				assert.NoDirExists(t, filepath.Join(dir, "vex"))
 			},
 		},
 		{
@@ -127,6 +150,7 @@ func createTestFiles(t *testing.T, dir string) {
 		"db",
 		"java-db",
 		"policy",
+		"vex",
 	}
 	for _, subdir := range subdirs {
 		err := os.MkdirAll(filepath.Join(dir, subdir), 0755)