diff --git a/bootstrap/bootstrap.go b/bootstrap/bootstrap.go
index e7f1d03..081abab 100644
--- a/bootstrap/bootstrap.go
+++ b/bootstrap/bootstrap.go
@@ -205,6 +205,11 @@ func normalize(opts Options) Options {
 	}
 	opts.Aliases = normalizeAliases(opts.Aliases, opts.EnableDoctorAlias)
 	opts.AliasDescriptions = normalizeAliasDescriptions(opts.AliasDescriptions, opts.Aliases, opts.EnableDoctorAlias)
+	for _, cmd := range autoDisabledCommands(opts) {
+		if !isCommandDisabled(cmd, opts.DisabledCommands) {
+			opts.DisabledCommands = append(opts.DisabledCommands, cmd)
+		}
+	}
 	return opts
 }
 
@@ -461,14 +466,14 @@ func printHelp(opts Options, command string, args ...[]string) error {
 		return printGlobalHelp(opts)
 	}
 
-	if command == CommandConfig {
-		return printConfigHelp(opts, commandArgs)
-	}
-
 	if isCommandDisabled(command, opts.DisabledCommands) {
 		return fmt.Errorf("%w: %s", ErrUnknownCommand, command)
 	}
 
+	if command == CommandConfig {
+		return printConfigHelp(opts, commandArgs)
+	}
+
 	for _, def := range commands {
 		if def.Name != command {
 			continue
@@ -583,6 +588,30 @@ func printGlobalHelp(opts Options) error {
 	return err
 }
 
+func autoDisabledCommands(opts Options) []string {
+	h := opts.Hooks
+	var disabled []string
+	if h.Setup == nil {
+		disabled = append(disabled, CommandSetup)
+	}
+	if h.Login == nil {
+		disabled = append(disabled, CommandLogin)
+	}
+	if h.MCP == nil {
+		disabled = append(disabled, CommandMCP)
+	}
+	if h.Config == nil && h.ConfigShow == nil && h.ConfigTest == nil && h.ConfigDelete == nil {
+		disabled = append(disabled, CommandConfig)
+	}
+	if h.Update == nil {
+		disabled = append(disabled, CommandUpdate)
+	}
+	if h.Version == nil && strings.TrimSpace(opts.Version) == "" {
+		disabled = append(disabled, CommandVersion)
+	}
+	return disabled
+}
+
 func isCommandDisabled(command string, disabled []string) bool {
 	for _, d := range disabled {
 		if d == command {
diff --git a/bootstrap/bootstrap_test.go b/bootstrap/bootstrap_test.go
index f0fbbeb..9bd642f 100644
--- a/bootstrap/bootstrap_test.go
+++ b/bootstrap/bootstrap_test.go
@@ -91,11 +91,13 @@ func TestRunReturnsCommandNotConfigured(t *testing.T) {
 	var stdout bytes.Buffer
 	var stderr bytes.Buffer
 
+	noop := func(_ context.Context, _ Invocation) error { return nil }
 	err := Run(context.Background(), Options{
 		BinaryName: "my-mcp",
 		Args:       []string{"config"},
 		Stdout:     &stdout,
 		Stderr:     &stderr,
+		Hooks:      Hooks{ConfigShow: noop},
 	})
 	if !errors.Is(err, ErrSubcommandRequired) {
 		t.Fatalf("Run error = %v, want ErrSubcommandRequired", err)
@@ -148,7 +150,7 @@ func TestRunVersionHookOverridesDefault(t *testing.T) {
 	}
 }
 
-func TestRunRequiresVersionWithoutVersionHook(t *testing.T) {
+func TestRunVersionAutoHiddenWithoutHookOrVersionString(t *testing.T) {
 	var stdout bytes.Buffer
 	var stderr bytes.Buffer
 
@@ -158,8 +160,8 @@ func TestRunRequiresVersionWithoutVersionHook(t *testing.T) {
 		Stdout:     &stdout,
 		Stderr:     &stderr,
 	})
-	if !errors.Is(err, ErrVersionRequired) {
-		t.Fatalf("Run error = %v, want ErrVersionRequired", err)
+	if !errors.Is(err, ErrUnknownCommand) {
+		t.Fatalf("Run error = %v, want ErrUnknownCommand", err)
 	}
 }
 
@@ -167,12 +169,15 @@ func TestRunPrintsGlobalHelp(t *testing.T) {
 	var stdout bytes.Buffer
 	var stderr bytes.Buffer
 
+	noop := func(_ context.Context, _ Invocation) error { return nil }
 	err := Run(context.Background(), Options{
 		BinaryName:  "my-mcp",
 		Description: "Binaire MCP de test.",
+		Version:     "v1.2.3",
 		Args:        []string{"help"},
 		Stdout:      &stdout,
 		Stderr:      &stderr,
+		Hooks:       Hooks{Setup: noop, MCP: noop, ConfigShow: noop, Update: noop},
 	})
 	if err != nil {
 		t.Fatalf("Run error = %v", err)
@@ -197,12 +202,15 @@ func TestRunPrintsGlobalHelpWhenNoArgs(t *testing.T) {
 	var stdout bytes.Buffer
 	var stderr bytes.Buffer
 
+	noop := func(_ context.Context, _ Invocation) error { return nil }
 	err := Run(context.Background(), Options{
 		BinaryName:  "my-mcp",
 		Description: "Binaire MCP de test.",
+		Version:     "v1.2.3",
 		Args:        []string{},
 		Stdout:      &stdout,
 		Stderr:      &stderr,
+		Hooks:       Hooks{Setup: noop, MCP: noop, ConfigShow: noop, Update: noop},
 	})
 	if err != nil {
 		t.Fatalf("Run error = %v", err)
@@ -227,11 +235,13 @@ func TestRunPrintsCommandHelp(t *testing.T) {
 	var stdout bytes.Buffer
 	var stderr bytes.Buffer
 
+	noop := func(_ context.Context, _ Invocation) error { return nil }
 	err := Run(context.Background(), Options{
 		BinaryName: "my-mcp",
 		Args:       []string{"help", "update"},
 		Stdout:     &stdout,
 		Stderr:     &stderr,
+		Hooks:      Hooks{Update: noop},
 	})
 	if err != nil {
 		t.Fatalf("Run error = %v", err)
@@ -250,11 +260,13 @@ func TestRunPrintsLoginCommandHelp(t *testing.T) {
 	var stdout bytes.Buffer
 	var stderr bytes.Buffer
 
+	noop := func(_ context.Context, _ Invocation) error { return nil }
 	err := Run(context.Background(), Options{
 		BinaryName: "my-mcp",
 		Args:       []string{"help", "login"},
 		Stdout:     &stdout,
 		Stderr:     &stderr,
+		Hooks:      Hooks{Login: noop},
 	})
 	if err != nil {
 		t.Fatalf("Run error = %v", err)
@@ -273,11 +285,13 @@ func TestRunPrintsConfigHelp(t *testing.T) {
 	var stdout bytes.Buffer
 	var stderr bytes.Buffer
 
+	noop := func(_ context.Context, _ Invocation) error { return nil }
 	err := Run(context.Background(), Options{
 		BinaryName: "my-mcp",
 		Args:       []string{"help", "config"},
 		Stdout:     &stdout,
 		Stderr:     &stderr,
+		Hooks:      Hooks{ConfigShow: noop},
 	})
 	if err != nil {
 		t.Fatalf("Run error = %v", err)
@@ -299,11 +313,13 @@ func TestRunPrintsConfigSubcommandHelp(t *testing.T) {
 	var stdout bytes.Buffer
 	var stderr bytes.Buffer
 
+	noop := func(_ context.Context, _ Invocation) error { return nil }
 	err := Run(context.Background(), Options{
 		BinaryName: "my-mcp",
 		Args:       []string{"help", "config", "show"},
 		Stdout:     &stdout,
 		Stderr:     &stderr,
+		Hooks:      Hooks{ConfigShow: noop},
 	})
 	if err != nil {
 		t.Fatalf("Run error = %v", err)
@@ -349,11 +365,13 @@ func TestRunConfigShowReturnsCommandNotConfigured(t *testing.T) {
 	var stdout bytes.Buffer
 	var stderr bytes.Buffer
 
+	noop := func(_ context.Context, _ Invocation) error { return nil }
 	err := Run(context.Background(), Options{
 		BinaryName: "my-mcp",
 		Args:       []string{"config", "show"},
 		Stdout:     &stdout,
 		Stderr:     &stderr,
+		Hooks:      Hooks{ConfigTest: noop},
 	})
 	if !errors.Is(err, ErrCommandNotConfigured) {
 		t.Fatalf("Run error = %v, want ErrCommandNotConfigured", err)
@@ -364,11 +382,13 @@ func TestRunConfigReturnsUnknownSubcommand(t *testing.T) {
 	var stdout bytes.Buffer
 	var stderr bytes.Buffer
 
+	noop := func(_ context.Context, _ Invocation) error { return nil }
 	err := Run(context.Background(), Options{
 		BinaryName: "my-mcp",
 		Args:       []string{"config", "sync"},
 		Stdout:     &stdout,
 		Stderr:     &stderr,
+		Hooks:      Hooks{ConfigShow: noop},
 	})
 	if !errors.Is(err, ErrUnknownSubcommand) {
 		t.Fatalf("Run error = %v, want ErrUnknownSubcommand", err)
@@ -412,6 +432,7 @@ func TestRunPrintsAliasHelpFromHelpCommand(t *testing.T) {
 	var stdout bytes.Buffer
 	var stderr bytes.Buffer
 
+	noop := func(_ context.Context, _ Invocation) error { return nil }
 	err := Run(context.Background(), Options{
 		BinaryName: "my-mcp",
 		Aliases: map[string][]string{
@@ -420,6 +441,7 @@ func TestRunPrintsAliasHelpFromHelpCommand(t *testing.T) {
 		Args:   []string{"help", "doctor"},
 		Stdout: &stdout,
 		Stderr: &stderr,
+		Hooks:  Hooks{ConfigTest: noop},
 	})
 	if err != nil {
 		t.Fatalf("Run error = %v", err)
@@ -435,6 +457,7 @@ func TestRunPrintsAliasHelpFromTrailingHelpFlag(t *testing.T) {
 	var stdout bytes.Buffer
 	var stderr bytes.Buffer
 
+	noop := func(_ context.Context, _ Invocation) error { return nil }
 	err := Run(context.Background(), Options{
 		BinaryName: "my-mcp",
 		Aliases: map[string][]string{
@@ -443,6 +466,7 @@ func TestRunPrintsAliasHelpFromTrailingHelpFlag(t *testing.T) {
 		Args:   []string{"doctor", "--help"},
 		Stdout: &stdout,
 		Stderr: &stderr,
+		Hooks:  Hooks{ConfigTest: noop},
 	})
 	if err != nil {
 		t.Fatalf("Run error = %v", err)