diff --git a/clustertool/cmd/genconfig.go b/clustertool/cmd/genconfig.go
index 8b60fed56fa49..9b500f5ee6141 100644
--- a/clustertool/cmd/genconfig.go
+++ b/clustertool/cmd/genconfig.go
@@ -3,10 +3,8 @@ package cmd
 import (
     "strings"
 
-    "github.com/rs/zerolog/log"
     "github.com/spf13/cobra"
     "github.com/truecharts/public/clustertool/pkg/gencmd"
-    "github.com/truecharts/public/clustertool/pkg/sops"
 )
 
 var genConfigLongHelp = strings.TrimSpace(`
@@ -24,9 +22,6 @@ var genConfig = &cobra.Command{
     Long:    genConfigLongHelp,
     Example: "clustertool genconfig",
     Run: func(cmd *cobra.Command, args []string) {
-        if err := sops.DecryptFiles(); err != nil {
-            log.Info().Msgf("Error decrypting files: %v\n", err)
-        }
 
         gencmd.GenConfig(args)
     },
diff --git a/clustertool/pkg/gencmd/bootstrap.go b/clustertool/pkg/gencmd/bootstrap.go
index 5f3fb79cb95a5..e842c0ef9ecad 100644
--- a/clustertool/pkg/gencmd/bootstrap.go
+++ b/clustertool/pkg/gencmd/bootstrap.go
@@ -28,9 +28,11 @@ func RunBootstrap(args []string) {
     if len(args) > 1 {
         extraArgs = args[1:]
     }
+
     if err := sops.DecryptFiles(); err != nil {
         log.Info().Msgf("Error decrypting files: %v\n", err)
     }
+
     bootstrapNode := talassist.TalConfig.Nodes[0].IPAddress
     bootstrapcmds := GenPlain("bootstrap", bootstrapNode, extraArgs)
 
diff --git a/clustertool/pkg/gencmd/genconfig.go b/clustertool/pkg/gencmd/genconfig.go
index da8f731dcfb9d..eb44478c39663 100644
--- a/clustertool/pkg/gencmd/genconfig.go
+++ b/clustertool/pkg/gencmd/genconfig.go
@@ -11,10 +11,18 @@ import (
     "github.com/truecharts/public/clustertool/pkg/fluxhandler"
     "github.com/truecharts/public/clustertool/pkg/helper"
     "github.com/truecharts/public/clustertool/pkg/initfiles"
+    "github.com/truecharts/public/clustertool/pkg/sops"
     "github.com/truecharts/public/clustertool/pkg/talassist"
 )
 
 func GenConfig(args []string) error {
+    if initfiles.CheckRunAgainFileExists() {
+        log.Fatal().Msg("You need to re-run Init. Exiting...")
+        os.Exit(1)
+    }
+    if err := sops.DecryptFiles(); err != nil {
+        log.Info().Msgf("Error decrypting files: %v\n", err)
+    }
     talassist.LoadTalConfig()
     talassist.GenSchema()
     initfiles.GenTalEnvConfigMap()
diff --git a/clustertool/pkg/initfiles/initfiles.go b/clustertool/pkg/initfiles/initfiles.go
index 60736f0eb278c..9b92fe22e3b51 100644
--- a/clustertool/pkg/initfiles/initfiles.go
+++ b/clustertool/pkg/initfiles/initfiles.go
@@ -23,6 +23,7 @@ import (
 )
 
 func InitFiles() error {
+    removeRunAgainFile()
     ageGen()
     genRootFiles()
     genBaseFiles()
@@ -145,6 +146,7 @@ func genBaseFiles() error {
         clusterEnvPresent = true
         log.Debug().Msg("Detected existing cluster, continuing")
     } else if os.IsNotExist(err) {
+        createRunAgainFile()
         log.Warn().Msg("New cluster detected, creating clusterenv.yaml\n Please fill out ClusterEnv.yaml and run init again!")
     } else {
         log.Fatal().Err(err).Msgf("Error checking clusterenv file: %s", err)
@@ -166,6 +168,38 @@ func genBaseFiles() error {
     return nil
 }
 
+// Create the "RUNAGAIN" file
+func createRunAgainFile() {
+    file, err := os.Create("RUNAGAIN")
+    if err != nil {
+        log.Err(err).Msg("error creating runagain file...")
+        return
+    }
+    defer file.Close()
+    return
+}
+
+// Remove the "RUNAGAIN" file if it exists
+func removeRunAgainFile() error {
+    if CheckRunAgainFileExists() {
+        err := os.Remove("RUNAGAIN")
+        if err != nil {
+            log.Err(err).Msg("error removing runagain file...")
+            return err
+        }
+        log.Debug().Msg("RUNAGAIN file removed.")
+    } else {
+        log.Debug().Msg("RUNAGAIN file does not exist.")
+    }
+    return nil
+}
+
+// Check if the "RUNAGAIN" file exists
+func CheckRunAgainFileExists() bool {
+    _, err := os.Stat("RUNAGAIN")
+    return !os.IsNotExist(err)
+}
+
 func UpdateBaseFiles() error {
     log.Info().Msg("Updating Base files for cluster: helper.ClusterPath")
     // Read filenames in source directory