diff --git a/cmd/flux/bootstrap.go b/cmd/flux/bootstrap.go
index 7f92ca51..fd53ddc0 100644
--- a/cmd/flux/bootstrap.go
+++ b/cmd/flux/bootstrap.go
@@ -266,3 +266,20 @@ func generateDeployKey(ctx context.Context, kubeClient client.Client, url *url.U
 
 	return string(pair.PublicKey), nil
 }
+
+func checkIfBootstrapPathDiffers(ctx context.Context, kubeClient client.Client, namespace string, path string) bool {
+	namespacedName := types.NamespacedName{
+		Name:      namespace,
+		Namespace: namespace,
+	}
+	var fluxSystemKustomization kustomizev1.Kustomization
+	err := kubeClient.Get(ctx, namespacedName, &fluxSystemKustomization)
+	if err != nil {
+		return false
+	}
+	if fluxSystemKustomization.Spec.Path == path {
+		return false
+	}
+
+	return true
+}
diff --git a/cmd/flux/bootstrap_github.go b/cmd/flux/bootstrap_github.go
index b9cf8450..2a12991d 100644
--- a/cmd/flux/bootstrap_github.go
+++ b/cmd/flux/bootstrap_github.go
@@ -115,6 +115,20 @@ func bootstrapGitHubCmdRun(cmd *cobra.Command, args []string) error {
 		return err
 	}
 
+	ctx, cancel := context.WithTimeout(context.Background(), timeout)
+	defer cancel()
+
+	kubeClient, err := utils.KubeClient(kubeconfig, kubecontext)
+	if err != nil {
+		return err
+	}
+
+	bootstrapPathDiffers := checkIfBootstrapPathDiffers(ctx, kubeClient, namespace, filepath.ToSlash(ghPath.String()))
+
+	if bootstrapPathDiffers {
+		return fmt.Errorf("cluster already bootstrapped to a different path")
+	}
+
 	repository, err := git.NewRepository(ghRepository, ghOwner, ghHostname, ghToken, "flux", ghOwner+"@users.noreply.github.com")
 	if err != nil {
 		return err
@@ -135,9 +149,6 @@ func bootstrapGitHubCmdRun(cmd *cobra.Command, args []string) error {
 	}
 	defer os.RemoveAll(tmpDir)
 
-	ctx, cancel := context.WithTimeout(context.Background(), timeout)
-	defer cancel()
-
 	if ghDelete {
 		if err := provider.DeleteRepository(ctx, repository); err != nil {
 			return err
@@ -198,11 +209,6 @@ func bootstrapGitHubCmdRun(cmd *cobra.Command, args []string) error {
 		logger.Successf("components are up to date")
 	}
 
-	kubeClient, err := utils.KubeClient(kubeconfig, kubecontext)
-	if err != nil {
-		return err
-	}
-
 	// determine if repo synchronization is working
 	isInstall := shouldInstallManifests(ctx, kubeClient, namespace)
 
diff --git a/cmd/flux/bootstrap_gitlab.go b/cmd/flux/bootstrap_gitlab.go
index e8b9556c..63677466 100644
--- a/cmd/flux/bootstrap_gitlab.go
+++ b/cmd/flux/bootstrap_gitlab.go
@@ -115,6 +115,20 @@ func bootstrapGitLabCmdRun(cmd *cobra.Command, args []string) error {
 		return err
 	}
 
+	ctx, cancel := context.WithTimeout(context.Background(), timeout)
+	defer cancel()
+
+	kubeClient, err := utils.KubeClient(kubeconfig, kubecontext)
+	if err != nil {
+		return err
+	}
+
+	bootstrapPathDiffers := checkIfBootstrapPathDiffers(ctx, kubeClient, namespace, filepath.ToSlash(glPath.String()))
+
+	if bootstrapPathDiffers {
+		return fmt.Errorf("cluster already bootstrapped to a different path")
+	}
+
 	repository, err := git.NewRepository(glRepository, glOwner, glHostname, glToken, "flux", glOwner+"@users.noreply.gitlab.com")
 	if err != nil {
 		return err
@@ -129,20 +143,12 @@ func bootstrapGitLabCmdRun(cmd *cobra.Command, args []string) error {
 		IsPersonal: glPersonal,
 	}
 
-	kubeClient, err := utils.KubeClient(kubeconfig, kubecontext)
-	if err != nil {
-		return err
-	}
-
 	tmpDir, err := ioutil.TempDir("", namespace)
 	if err != nil {
 		return err
 	}
 	defer os.RemoveAll(tmpDir)
 
-	ctx, cancel := context.WithTimeout(context.Background(), timeout)
-	defer cancel()
-
 	// create GitLab project if doesn't exists
 	logger.Actionf("connecting to %s", glHostname)
 	changed, err := provider.CreateRepository(ctx, repository)