diff --git a/clustertool/cmd/root.go b/clustertool/cmd/root.go
index cc2fd1f3877..f7e820734cb 100644
--- a/clustertool/cmd/root.go
+++ b/clustertool/cmd/root.go
@@ -36,6 +36,7 @@ func Execute() error {
         helper.ClusterEnvFile = filepath.Join(helper.ClusterPath, "/clusterenv.yaml")
         helper.TalConfigFile = filepath.Join(helper.ClusterPath, "/talos", "talconfig.yaml")
         helper.TalosPath = filepath.Join(helper.ClusterPath, "/talos")
+        helper.KubernetesPath = filepath.Join(helper.ClusterPath, "/kubernetes")
         helper.TalosGenerated = filepath.Join(helper.TalosPath, "/generated")
         helper.TalosConfigFile = filepath.Join(helper.TalosGenerated, "talosconfig")
         helper.TalSecretFile = filepath.Join(helper.TalosGenerated, "talsecret.yaml")
diff --git a/clustertool/pkg/gencmd/bootstrap.go b/clustertool/pkg/gencmd/bootstrap.go
index 651c01fe966..f9cc3d2ade4 100644
--- a/clustertool/pkg/gencmd/bootstrap.go
+++ b/clustertool/pkg/gencmd/bootstrap.go
@@ -21,6 +21,12 @@ import (
 
 var HelmRepos map[string]*fluxhandler.HelmRepo
 
+var manifestPaths = []string{
+    filepath.Join(helper.KubernetesPath, "flux-system", "flux", "sopssecret.secret.yaml"),
+    filepath.Join(helper.KubernetesPath, "flux-system", "flux", "deploykey.secret.yaml"),
+    filepath.Join(helper.KubernetesPath, "flux-system", "flux", "clustersettings.secret.yaml"),
+}
+
 func GenBootstrap(node string, extraFlags []string) string {
     cfg, err := talhelperCfg.LoadAndValidateFromFile(helper.TalConfigFile, []string{helper.ClusterEnvFile}, false)
     if err != nil {
@@ -158,7 +164,7 @@ func RunBootstrap(args []string) {
         }
     }
 
-    for _, filePath := range helper.ManifestPaths {
+    for _, filePath := range manifestPaths {
         log.Info().Msgf("Bootstrap: Loading Manifest: %v", filePath)
         if err := kubectlcmds.KubectlApply(ctx, filePath); err != nil {
             log.Info().Msgf("Error applying manifest for %s: %v\n", filepath.Base(filePath), err)
diff --git a/clustertool/pkg/helper/vars.go b/clustertool/pkg/helper/vars.go
index 52c567164aa..18772a686da 100644
--- a/clustertool/pkg/helper/vars.go
+++ b/clustertool/pkg/helper/vars.go
@@ -27,11 +27,6 @@ var (
     AllIPs          = []string{}
     ControlPlaneIPs = []string{}
     WorkerIPs       = []string{}
-    ManifestPaths   = []string{
-        filepath.Join(KubernetesPath, "flux-system", "flux", "sopssecret.secret.yaml"),
-        filepath.Join(KubernetesPath, "flux-system", "flux", "deploykey.secret.yaml"),
-        filepath.Join(KubernetesPath, "flux-system", "flux", "clustersettings.secret.yaml"),
-    }
 
     KubeFilterStr = []string{
         ".*would violate PodSecurity.*",