diff --git a/cmd/docker-mcp/commands/catalog_next.go b/cmd/docker-mcp/commands/catalog_next.go
index 42ee735d..23162a6f 100644
--- a/cmd/docker-mcp/commands/catalog_next.go
+++ b/cmd/docker-mcp/commands/catalog_next.go
@@ -9,25 +9,14 @@ import (
 
 	catalognext "github.com/docker/mcp-gateway/pkg/catalog_next"
 	"github.com/docker/mcp-gateway/pkg/db"
-	"github.com/docker/mcp-gateway/pkg/docker"
-	"github.com/docker/mcp-gateway/pkg/migrate"
 	"github.com/docker/mcp-gateway/pkg/oci"
 	"github.com/docker/mcp-gateway/pkg/workingset"
 )
 
-func catalogNextCommand(docker docker.Client) *cobra.Command {
+func catalogNextCommand() *cobra.Command {
 	cmd := &cobra.Command{
 		Use:   "catalog-next",
 		Short: "Manage catalogs (next generation)",
-		PersistentPreRunE: func(cmd *cobra.Command, _ []string) error {
-			dao, err := db.New()
-			if err != nil {
-				return err
-			}
-			defer dao.Close()
-			migrate.MigrateConfig(cmd.Context(), docker, dao)
-			return nil
-		},
 	}
 
 	cmd.AddCommand(createCatalogNextCommand())
diff --git a/cmd/docker-mcp/commands/root.go b/cmd/docker-mcp/commands/root.go
index 24bf6eaf..e9d5a441 100644
--- a/cmd/docker-mcp/commands/root.go
+++ b/cmd/docker-mcp/commands/root.go
@@ -3,14 +3,17 @@ package commands
 import (
 	"context"
 	"os"
+	"slices"
 
 	"github.com/docker/cli/cli-plugins/plugin"
 	"github.com/docker/cli/cli/command"
 	"github.com/spf13/cobra"
 
 	"github.com/docker/mcp-gateway/cmd/docker-mcp/version"
+	"github.com/docker/mcp-gateway/pkg/db"
 	"github.com/docker/mcp-gateway/pkg/desktop"
 	"github.com/docker/mcp-gateway/pkg/docker"
+	"github.com/docker/mcp-gateway/pkg/migrate"
 )
 
 // Note: We use a custom help template to make it more brief.
@@ -31,6 +34,8 @@ Examples:
 
 // Root returns the root command for the init plugin
 func Root(ctx context.Context, cwd string, dockerCli command.Cli) *cobra.Command {
+	dockerClient := docker.NewClient(dockerCli)
+
 	cmd := &cobra.Command{
 		Use:              "mcp [OPTIONS]",
 		Short:            "Manage MCP servers and clients",
@@ -46,6 +51,17 @@ func Root(ctx context.Context, cwd string, dockerCli command.Cli) *cobra.Command
 			}
 
 			if os.Getenv("DOCKER_MCP_IN_CONTAINER") != "1" {
+				if isWorkingSetsFeatureEnabled(dockerCli) {
+					if isSubcommandOf(cmd, []string{"catalog-next", "catalog", "profile"}) {
+						dao, err := db.New()
+						if err != nil {
+							return err
+						}
+						defer dao.Close()
+						migrate.MigrateConfig(cmd.Context(), dockerClient, dao)
+					}
+				}
+
 				runningInDockerCE, err := docker.RunningInDockerCE(ctx, dockerCli)
 				if err != nil {
 					return err
@@ -68,11 +84,9 @@ func Root(ctx context.Context, cwd string, dockerCli command.Cli) *cobra.Command
 		return []string{"--help"}, cobra.ShellCompDirectiveNoFileComp
 	})
 
-	dockerClient := docker.NewClient(dockerCli)
-
 	if isWorkingSetsFeatureEnabled(dockerCli) {
-		cmd.AddCommand(workingSetCommand(dockerClient))
-		cmd.AddCommand(catalogNextCommand(dockerClient))
+		cmd.AddCommand(workingSetCommand())
+		cmd.AddCommand(catalogNextCommand())
 	}
 	cmd.AddCommand(catalogCommand(dockerCli))
 	cmd.AddCommand(clientCommand(dockerCli, cwd))
@@ -101,3 +115,15 @@ func unhideHiddenCommands(cmd *cobra.Command) {
 		unhideHiddenCommands(c)
 	}
 }
+
+func isSubcommandOf(cmd *cobra.Command, names []string) bool {
+	if cmd == nil {
+		return false
+	}
+
+	if slices.Contains(names, cmd.Name()) {
+		return true
+	}
+
+	return isSubcommandOf(cmd.Parent(), names)
+}
diff --git a/cmd/docker-mcp/commands/workingset.go b/cmd/docker-mcp/commands/workingset.go
index d1482014..f30576cf 100644
--- a/cmd/docker-mcp/commands/workingset.go
+++ b/cmd/docker-mcp/commands/workingset.go
@@ -9,29 +9,18 @@ import (
 
 	"github.com/docker/mcp-gateway/pkg/client"
 	"github.com/docker/mcp-gateway/pkg/db"
-	"github.com/docker/mcp-gateway/pkg/docker"
-	"github.com/docker/mcp-gateway/pkg/migrate"
 	"github.com/docker/mcp-gateway/pkg/oci"
 	"github.com/docker/mcp-gateway/pkg/registryapi"
 	"github.com/docker/mcp-gateway/pkg/sliceutil"
 	"github.com/docker/mcp-gateway/pkg/workingset"
 )
 
-func workingSetCommand(docker docker.Client) *cobra.Command {
+func workingSetCommand() *cobra.Command {
 	cfg := client.ReadConfig()
 
 	cmd := &cobra.Command{
 		Use:   "profile",
 		Short: "Manage profiles",
-		PersistentPreRunE: func(cmd *cobra.Command, _ []string) error {
-			dao, err := db.New()
-			if err != nil {
-				return err
-			}
-			defer dao.Close()
-			migrate.MigrateConfig(cmd.Context(), docker, dao)
-			return nil
-		},
 	}
 
 	cmd.AddCommand(exportWorkingSetCommand())