diff --git a/cmd/internal/flags.go b/cmd/internal/flags.go
index f8038ac86494..ed8f4e35b7ca 100644
--- a/cmd/internal/flags.go
+++ b/cmd/internal/flags.go
@@ -42,7 +42,7 @@ func PersistentFlags(parentCmd *cobra.Command, opts *ToolboxOptions) {
 
 // ConfigFileFlags defines flags related to the configuration file.
 // It should be applied to any command that requires configuration loading.
-func ConfigFileFlags(flags *pflag.FlagSet, opts *ToolboxOptions) {
+func ConfigFileFlags(parentCmd *cobra.Command, flags *pflag.FlagSet, opts *ToolboxOptions) {
 	flags.StringVar(&opts.Config, "config", "", "File path specifying the tool configuration. Cannot be used with --configs, or --config-folder.")
 	flags.StringVar(&opts.Config, "tools-file", "", "File path specifying the tool configuration. Cannot be used with --tools-files, or --tools-folder.")
 	_ = flags.MarkDeprecated("tools-file", "please use --config instead") // DEPRECATED
@@ -52,6 +52,7 @@ func ConfigFileFlags(flags *pflag.FlagSet, opts *ToolboxOptions) {
 	flags.StringVar(&opts.ConfigFolder, "config-folder", "", "Directory path containing YAML tool configuration files. All .yaml and .yml files in the directory will be loaded and merged. Cannot be used with --config, or --configs.")
 	flags.StringVar(&opts.ConfigFolder, "tools-folder", "", "Directory path containing YAML tool configuration files. All .yaml and .yml files in the directory will be loaded and merged. Cannot be used with --tools-file, or --tools-files.")
 	_ = flags.MarkDeprecated("tools-folder", "please use --config-folder instead") // DEPRECATED
+	parentCmd.MarkFlagsMutuallyExclusive("config", "configs", "config-folder", "tools-file", "tools-files", "tools-folder")
 	// Fetch prebuilt tools sources to customize the help description
 	prebuiltHelp := fmt.Sprintf(
 		"Use a prebuilt tool configuration by source type. Allowed: '%s'. Can be specified multiple times.",
diff --git a/cmd/internal/invoke/command.go b/cmd/internal/invoke/command.go
index 531fbfcfd70c..714318bd1738 100644
--- a/cmd/internal/invoke/command.go
+++ b/cmd/internal/invoke/command.go
@@ -42,7 +42,7 @@ Example:
 		},
 	}
 	flags := cmd.Flags()
-	internal.ConfigFileFlags(flags, opts)
+	internal.ConfigFileFlags(cmd, flags, opts)
 	return cmd
 }
 
diff --git a/cmd/internal/migrate/command.go b/cmd/internal/migrate/command.go
index a5b6489b41ed..3c7f64e0b673 100644
--- a/cmd/internal/migrate/command.go
+++ b/cmd/internal/migrate/command.go
@@ -39,7 +39,7 @@ func NewCommand(opts *internal.ToolboxOptions) *cobra.Command {
 		Long:  "Migrate all configuration files provided to the flat format, updating deprecated fields and ensuring compatibility.",
 	}
 	flags := cmd.Flags()
-	internal.ConfigFileFlags(flags, opts)
+	internal.ConfigFileFlags(cmd.Command, flags, opts)
 	flags.BoolVar(&cmd.dryRun, "dry-run", false, "Preview the converted format without applying actual changes.")
 	cmd.RunE = func(*cobra.Command, []string) error { return runMigrate(cmd, opts) }
 	return cmd.Command
diff --git a/cmd/internal/options.go b/cmd/internal/options.go
index 3affd3aaf4ee..d1f648c7c907 100644
--- a/cmd/internal/options.go
+++ b/cmd/internal/options.go
@@ -148,15 +148,6 @@ func (opts *ToolboxOptions) GetCustomConfigFiles(ctx context.Context) ([]string,
 
 	// Load Custom Configurations
 	if isCustomConfigured {
-		// Enforce exclusivity among custom flags (tools-file vs tools-files vs tools-folder)
-		if (opts.Config != "" && len(opts.Configs) > 0) ||
-			(opts.Config != "" && opts.ConfigFolder != "") ||
-			(len(opts.Configs) > 0 && opts.ConfigFolder != "") {
-			errMsg := fmt.Errorf("--config/--tools-file, --configs/--tools-files, and --config-folder/--tools-folder flags cannot be used simultaneously")
-			logger.ErrorContext(ctx, errMsg.Error())
-			return nil, isCustomConfigured, errMsg
-		}
-
 		if len(opts.Configs) > 0 {
 			// Use tools-files
 			logger.InfoContext(ctx, fmt.Sprintf("retrieving %d tool configuration files", len(opts.Configs)))
diff --git a/cmd/internal/skills/command.go b/cmd/internal/skills/command.go
index a51196c0de9f..68d26679eec5 100644
--- a/cmd/internal/skills/command.go
+++ b/cmd/internal/skills/command.go
@@ -57,7 +57,7 @@ func NewCommand(opts *internal.ToolboxOptions) *cobra.Command {
 	}
 
 	flags := cmd.Flags()
-	internal.ConfigFileFlags(flags, opts)
+	internal.ConfigFileFlags(cmd.Command, flags, opts)
 	flags.StringVar(&cmd.name, "name", "", "Name of the generated skill.")
 	flags.StringVar(&cmd.description, "description", "", "Description of the generated skill")
 	flags.StringVar(&cmd.toolset, "toolset", "", "Name of the toolset to convert into a skill. If not provided, all tools will be included.")
diff --git a/cmd/root.go b/cmd/root.go
index d5d8f40e7de0..f8233ea7e313 100644
--- a/cmd/root.go
+++ b/cmd/root.go
@@ -115,7 +115,7 @@ func NewCommand(opts *internal.ToolboxOptions) *cobra.Command {
 	// setup flags that are common across all commands
 	internal.PersistentFlags(cmd, opts)
 	flags := cmd.Flags()
-	internal.ConfigFileFlags(flags, opts)
+	internal.ConfigFileFlags(cmd, flags, opts)
 	internal.ServeFlags(flags, opts)
 	flags.BoolVar(&opts.Cfg.DisableReload, "disable-reload", false, "Disables dynamic reloading of tools file.")
 	flags.BoolVar(&opts.Cfg.IgnoreUnknownTools, "ignore-unknown-tools", false, "Log warnings and skip unknown/unsupported tool types instead of failing to start.")
diff --git a/cmd/root_test.go b/cmd/root_test.go
index 263809844fb5..7c3cf1b19085 100644
--- a/cmd/root_test.go
+++ b/cmd/root_test.go
@@ -666,12 +666,12 @@ func TestMutuallyExclusiveFlags(t *testing.T) {
 		{
 			desc:      "--config and --configs",
 			args:      []string{"--config", "my.yaml", "--configs", "a.yaml,b.yaml"},
-			errString: "--config/--tools-file, --configs/--tools-files, and --config-folder/--tools-folder flags cannot be used simultaneously",
+			errString: "if any flags in the group [config configs config-folder tools-file tools-files tools-folder] are set none of the others can be; [config configs] were all set",
 		},
 		{
 			desc:      "--config-folder and --configs",
 			args:      []string{"--config-folder", "./", "--configs", "a.yaml,b.yaml"},
-			errString: "--config/--tools-file, --configs/--tools-files, and --config-folder/--tools-folder flags cannot be used simultaneously",
+			errString: "if any flags in the group [config configs config-folder tools-file tools-files tools-folder] are set none of the others can be; [config-folder configs] were all set",
 		},
 	}