diff --git a/apps/evm/cmd/cleanup_goheader.go b/apps/evm/cmd/cleanup_goheader.go
new file mode 100644
index 000000000..b5c75e6c9
--- /dev/null
+++ b/apps/evm/cmd/cleanup_goheader.go
@@ -0,0 +1,134 @@
+package cmd
+
+import (
+	"context"
+	"fmt"
+
+	ds "github.com/ipfs/go-datastore"
+	dsq "github.com/ipfs/go-datastore/query"
+	"github.com/spf13/cobra"
+
+	rollcmd "github.com/evstack/ev-node/pkg/cmd"
+	"github.com/evstack/ev-node/pkg/store"
+)
+
+const (
+	// go-header store prefixes used prior to the unified store migration
+	headerSyncPrefix = "/headerSync"
+	dataSyncPrefix   = "/dataSync"
+)
+
+// NewCleanupGoHeaderCmd creates a command to delete the legacy go-header store data.
+// This data is no longer needed after the migration to the unified store approach
+// where HeaderStoreAdapter and DataStoreAdapter read directly from the ev-node store.
+func NewCleanupGoHeaderCmd() *cobra.Command {
+	var dryRun bool
+
+	cmd := &cobra.Command{
+		Use:   "cleanup-goheader",
+		Short: "Delete legacy go-header store data from disk",
+		Long: `Delete the legacy go-header store data (headerSync and dataSync prefixes) from the database.
+
+This command removes data that was previously duplicated by the go-header library
+for P2P sync operations. After the migration to the unified store approach,
+this data is no longer needed as the HeaderStoreAdapter and DataStoreAdapter
+now read directly from the ev-node store.
+
+WARNING: Make sure the node is stopped before running this command.
+This operation is irreversible.`,
+		RunE: func(cmd *cobra.Command, args []string) error {
+			nodeConfig, err := rollcmd.ParseConfig(cmd)
+			if err != nil {
+				return err
+			}
+
+			goCtx := cmd.Context()
+			if goCtx == nil {
+				goCtx = context.Background()
+			}
+
+			// Open the database
+			rawDB, err := store.NewDefaultKVStore(nodeConfig.RootDir, nodeConfig.DBPath, evmDbName)
+			if err != nil {
+				return fmt.Errorf("failed to open database: %w", err)
+			}
+			defer func() {
+				if closeErr := rawDB.Close(); closeErr != nil {
+					cmd.Printf("Warning: failed to close database: %v\n", closeErr)
+				}
+			}()
+
+			// Delete headerSync prefix
+			headerCount, err := deletePrefix(goCtx, rawDB, headerSyncPrefix, dryRun)
+			if err != nil {
+				return fmt.Errorf("failed to delete headerSync data: %w", err)
+			}
+
+			// Delete dataSync prefix
+			dataCount, err := deletePrefix(goCtx, rawDB, dataSyncPrefix, dryRun)
+			if err != nil {
+				return fmt.Errorf("failed to delete dataSync data: %w", err)
+			}
+
+			totalCount := headerCount + dataCount
+
+			if dryRun {
+				cmd.Printf("Dry run: would delete %d keys (%d headerSync, %d dataSync)\n",
+					totalCount, headerCount, dataCount)
+			} else {
+				if totalCount == 0 {
+					cmd.Println("No legacy go-header store data found to delete.")
+				} else {
+					cmd.Printf("Successfully deleted %d keys (%d headerSync, %d dataSync)\n",
+						totalCount, headerCount, dataCount)
+				}
+			}
+
+			return nil
+		},
+	}
+
+	cmd.Flags().BoolVar(&dryRun, "dry-run", false, "show what would be deleted without actually deleting")
+
+	return cmd
+}
+
+// deletePrefix deletes all keys with the given prefix from the datastore.
+// Returns the number of keys deleted.
+func deletePrefix(ctx context.Context, db ds.Batching, prefix string, dryRun bool) (int, error) {
+	results, err := db.Query(ctx, dsq.Query{
+		Prefix:   prefix,
+		KeysOnly: true,
+	})
+	if err != nil {
+		return 0, fmt.Errorf("failed to query keys with prefix %s: %w", prefix, err)
+	}
+	defer results.Close()
+
+	count := 0
+	batch, err := db.Batch(ctx)
+	if err != nil {
+		return 0, fmt.Errorf("failed to create batch: %w", err)
+	}
+
+	for result := range results.Next() {
+		if result.Error != nil {
+			return count, fmt.Errorf("error iterating results: %w", result.Error)
+		}
+
+		if !dryRun {
+			if err := batch.Delete(ctx, ds.NewKey(result.Key)); err != nil {
+				return count, fmt.Errorf("failed to delete key %s: %w", result.Key, err)
+			}
+		}
+		count++
+	}
+
+	if !dryRun && count > 0 {
+		if err := batch.Commit(ctx); err != nil {
+			return count, fmt.Errorf("failed to commit batch delete: %w", err)
+		}
+	}
+
+	return count, nil
+}
diff --git a/apps/evm/main.go b/apps/evm/main.go
index 04168e4fc..647aa0bc9 100644
--- a/apps/evm/main.go
+++ b/apps/evm/main.go
@@ -28,6 +28,7 @@ func main() {
 		cmd.InitCmd(),
 		cmd.RunCmd,
 		cmd.NewRollbackCmd(),
+		cmd.NewCleanupGoHeaderCmd(),
 		rollcmd.VersionCmd,
 		rollcmd.NetInfoCmd,
 		rollcmd.StoreUnsafeCleanCmd,