diff --git a/cmd/github-mcp-server/main.go b/cmd/github-mcp-server/main.go
index 05c2c6e0b..6ca0fb23b 100644
--- a/cmd/github-mcp-server/main.go
+++ b/cmd/github-mcp-server/main.go
@@ -83,6 +83,7 @@ var (
 				Host:                 viper.GetString("host"),
 				Token:                token,
 				EnabledToolsets:      enabledToolsets,
+				StrictToolsets:       viper.GetBool("strict_toolsets"),
 				EnabledTools:         enabledTools,
 				EnabledFeatures:      enabledFeatures,
 				DynamicToolsets:      viper.GetBool("dynamic_toolsets"),
@@ -134,6 +135,7 @@ func init() {
 
 	// Add global flags that will be shared by all commands
 	rootCmd.PersistentFlags().StringSlice("toolsets", nil, github.GenerateToolsetsHelp())
+	rootCmd.PersistentFlags().Bool("strict-toolsets", false, "Fail startup if any configured toolset is unrecognized")
 	rootCmd.PersistentFlags().StringSlice("tools", nil, "Comma-separated list of specific tools to enable")
 	rootCmd.PersistentFlags().StringSlice("exclude-tools", nil, "Comma-separated list of tool names to disable regardless of other settings")
 	rootCmd.PersistentFlags().StringSlice("features", nil, "Comma-separated list of feature flags to enable")
@@ -156,6 +158,7 @@ func init() {
 
 	// Bind flag to viper
 	_ = viper.BindPFlag("toolsets", rootCmd.PersistentFlags().Lookup("toolsets"))
+	_ = viper.BindPFlag("strict_toolsets", rootCmd.PersistentFlags().Lookup("strict-toolsets"))
 	_ = viper.BindPFlag("tools", rootCmd.PersistentFlags().Lookup("tools"))
 	_ = viper.BindPFlag("exclude_tools", rootCmd.PersistentFlags().Lookup("exclude-tools"))
 	_ = viper.BindPFlag("features", rootCmd.PersistentFlags().Lookup("features"))
diff --git a/docs/toolsets-and-icons.md b/docs/toolsets-and-icons.md
index 9c26b4aa1..866383935 100644
--- a/docs/toolsets-and-icons.md
+++ b/docs/toolsets-and-icons.md
@@ -24,6 +24,22 @@ ToolsetMetadataRepos = inventory.ToolsetMetadata{
 | `Default` | `bool` | Whether this toolset is enabled by default |
 | `Icon` | `string` | Octicon name for visual representation in MCP clients |
 
+## Strict Toolset Validation
+
+By default, unknown toolset names are ignored and a warning is logged. To fail closed on typos or stale config, enable strict mode:
+
+```bash
+github-mcp-server stdio --toolsets=repos,isssues --strict-toolsets
+```
+
+Strict mode exits startup with a validation error when any configured toolset is unrecognized.
+
+### Migration Path
+
+1. Run once without strict mode and check logs for `unrecognized toolsets ignored`.
+2. Fix typos or remove unsupported toolset names.
+3. Re-run with `--strict-toolsets` (or `GITHUB_STRICT_TOOLSETS=true`) in CI/production.
+
 ## Adding Icons to Toolsets
 
 Icons help users quickly identify toolsets in MCP-compatible clients. We use [Primer Octicons](https://primer.style/foundations/icons) for all icons.
diff --git a/internal/ghmcp/server.go b/internal/ghmcp/server.go
index 5c4e7f6f1..967f7b9f7 100644
--- a/internal/ghmcp/server.go
+++ b/internal/ghmcp/server.go
@@ -181,6 +181,9 @@ type StdioServerConfig struct {
 	// See: https://github.com/github/github-mcp-server?tab=readme-ov-file#tool-configuration
 	EnabledToolsets []string
 
+	// StrictToolsets fails startup when configured toolsets are unrecognized.
+	StrictToolsets bool
+
 	// EnabledTools is a list of specific tools to enable (additive to toolsets)
 	// When specified, these tools are registered in addition to any specified toolset tools
 	EnabledTools []string
@@ -269,6 +272,7 @@ func RunStdioServer(cfg StdioServerConfig) error {
 		Host:              cfg.Host,
 		Token:             cfg.Token,
 		EnabledToolsets:   cfg.EnabledToolsets,
+		StrictToolsets:    cfg.StrictToolsets,
 		EnabledTools:      cfg.EnabledTools,
 		EnabledFeatures:   cfg.EnabledFeatures,
 		DynamicToolsets:   cfg.DynamicToolsets,
diff --git a/pkg/github/server.go b/pkg/github/server.go
index 06c12575d..351b6d293 100644
--- a/pkg/github/server.go
+++ b/pkg/github/server.go
@@ -30,6 +30,9 @@ type MCPServerConfig struct {
 	// See: https://github.com/github/github-mcp-server?tab=readme-ov-file#tool-configuration
 	EnabledToolsets []string
 
+	// StrictToolsets fails startup when configured toolsets are unrecognized.
+	StrictToolsets bool
+
 	// EnabledTools is a list of specific tools to enable (additive to toolsets)
 	// When specified, these tools are registered in addition to any specified toolset tools
 	EnabledTools []string
@@ -110,6 +113,9 @@ func NewMCPServer(ctx context.Context, cfg *MCPServerConfig, deps ToolDependenci
 	ghServer.AddReceivingMiddleware(addGitHubAPIErrorToContext)
 
 	if unrecognized := inv.UnrecognizedToolsets(); len(unrecognized) > 0 {
+		if cfg.StrictToolsets {
+			return nil, fmt.Errorf("strict toolset validation failed: unrecognized toolsets: %s", strings.Join(unrecognized, ", "))
+		}
 		cfg.Logger.Warn("Warning: unrecognized toolsets ignored", "toolsets", strings.Join(unrecognized, ", "))
 	}
 
diff --git a/pkg/github/server_test.go b/pkg/github/server_test.go
index 2b99cab12..4efb62c4b 100644
--- a/pkg/github/server_test.go
+++ b/pkg/github/server_test.go
@@ -5,6 +5,8 @@ import (
 	"encoding/json"
 	"errors"
 	"fmt"
+	"io"
+	"log/slog"
 	"net/http"
 	"testing"
 	"time"
@@ -219,3 +221,54 @@ func TestResolveEnabledToolsets(t *testing.T) {
 		})
 	}
 }
+
+func TestNewMCPServer_StrictToolsetsFailsOnUnknownToolset(t *testing.T) {
+	t.Parallel()
+
+	cfg := MCPServerConfig{
+		Version:           "test",
+		Token:             "test-token",
+		EnabledToolsets:   []string{"unknown-toolset"},
+		StrictToolsets:    true,
+		Translator:        translations.NullTranslationHelper,
+		ContentWindowSize: 5000,
+		Logger:            slog.New(slog.NewTextHandler(io.Discard, nil)),
+	}
+
+	inv, err := NewInventory(cfg.Translator).
+		WithDeprecatedAliases(DeprecatedToolAliases).
+		WithToolsets(cfg.EnabledToolsets).
+		Build()
+	require.NoError(t, err)
+	require.NotEmpty(t, inv.UnrecognizedToolsets())
+
+	_, err = NewMCPServer(context.Background(), &cfg, stubDeps{}, inv)
+	require.Error(t, err)
+	assert.Contains(t, err.Error(), "strict toolset validation failed")
+	assert.Contains(t, err.Error(), "unknown-toolset")
+}
+
+func TestNewMCPServer_NonStrictToolsetsAllowsUnknownToolset(t *testing.T) {
+	t.Parallel()
+
+	cfg := MCPServerConfig{
+		Version:           "test",
+		Token:             "test-token",
+		EnabledToolsets:   []string{"unknown-toolset"},
+		StrictToolsets:    false,
+		Translator:        translations.NullTranslationHelper,
+		ContentWindowSize: 5000,
+		Logger:            slog.New(slog.NewTextHandler(io.Discard, nil)),
+	}
+
+	inv, err := NewInventory(cfg.Translator).
+		WithDeprecatedAliases(DeprecatedToolAliases).
+		WithToolsets(cfg.EnabledToolsets).
+		Build()
+	require.NoError(t, err)
+	require.NotEmpty(t, inv.UnrecognizedToolsets())
+
+	server, err := NewMCPServer(context.Background(), &cfg, stubDeps{}, inv)
+	require.NoError(t, err)
+	require.NotNil(t, server)
+}