diff --git a/internal/ghmcp/server_test.go b/internal/ghmcp/server_test.go
index 04c0989d4..26c780c3e 100644
--- a/internal/ghmcp/server_test.go
+++ b/internal/ghmcp/server_test.go
@@ -1,8 +1,12 @@
 package ghmcp
 
 import (
+	"context"
+	"net/http"
+	"net/http/httptest"
 	"testing"
 
+	"github.com/github/github-mcp-server/pkg/github"
 	"github.com/github/github-mcp-server/pkg/translations"
 	"github.com/stretchr/testify/assert"
 	"github.com/stretchr/testify/require"
@@ -110,3 +114,127 @@ func TestResolveEnabledToolsets(t *testing.T) {
 		})
 	}
 }
+
+// TestBearerAuthTransport_AddsGraphQLFeaturesHeader verifies that the bearerAuthTransport
+// properly reads GraphQL features from context and adds them as a header.
+func TestBearerAuthTransport_AddsGraphQLFeaturesHeader(t *testing.T) {
+	t.Parallel()
+
+	tests := []struct {
+		name                string
+		features            []string
+		expectHeader        bool
+		expectedHeaderValue string
+	}{
+		{
+			name:                "single feature",
+			features:            []string{"issues_copilot_assignment_api_support"},
+			expectHeader:        true,
+			expectedHeaderValue: "issues_copilot_assignment_api_support",
+		},
+		{
+			name:                "multiple features",
+			features:            []string{"feature1", "feature2", "feature3"},
+			expectHeader:        true,
+			expectedHeaderValue: "feature1, feature2, feature3",
+		},
+		{
+			name:         "no features",
+			features:     []string{},
+			expectHeader: false,
+		},
+		{
+			name:         "nil features",
+			features:     nil,
+			expectHeader: false,
+		},
+	}
+
+	for _, tc := range tests {
+		t.Run(tc.name, func(t *testing.T) {
+			// Create a test server that records the request
+			var capturedRequest *http.Request
+			testServer := httptest.NewServer(http.HandlerFunc(func(w http.ResponseWriter, r *http.Request) {
+				capturedRequest = r
+				w.WriteHeader(http.StatusOK)
+			}))
+			defer testServer.Close()
+
+			// Create the transport chain
+			transport := &bearerAuthTransport{
+				transport: http.DefaultTransport,
+				token:     "test-token",
+			}
+
+			// Create an HTTP client with the transport
+			client := &http.Client{Transport: transport}
+
+			// Create a context with GraphQL features
+			ctx := context.Background()
+			if tc.features != nil {
+				ctx = github.WithGraphQLFeatures(ctx, tc.features...)
+			}
+
+			// Make a request with the context
+			req, err := http.NewRequestWithContext(ctx, "POST", testServer.URL, nil)
+			require.NoError(t, err)
+
+			resp, err := client.Do(req)
+			require.NoError(t, err)
+			defer resp.Body.Close()
+
+			// Verify the Authorization header is set
+			assert.Equal(t, "Bearer test-token", capturedRequest.Header.Get("Authorization"))
+
+			// Verify the GraphQL-Features header
+			if tc.expectHeader {
+				assert.Equal(t, tc.expectedHeaderValue, capturedRequest.Header.Get("GraphQL-Features"))
+			} else {
+				assert.Empty(t, capturedRequest.Header.Get("GraphQL-Features"))
+			}
+		})
+	}
+}
+
+// TestUserAgentTransport_PreservesGraphQLFeatures verifies that the userAgentTransport
+// doesn't interfere with GraphQL features set by bearerAuthTransport.
+func TestUserAgentTransport_PreservesGraphQLFeatures(t *testing.T) {
+	t.Parallel()
+
+	// Create a test server that records the request
+	var capturedRequest *http.Request
+	testServer := httptest.NewServer(http.HandlerFunc(func(w http.ResponseWriter, r *http.Request) {
+		capturedRequest = r
+		w.WriteHeader(http.StatusOK)
+	}))
+	defer testServer.Close()
+
+	// Create the transport chain (same as in production)
+	// userAgentTransport -> bearerAuthTransport -> http.DefaultTransport
+	transport := &userAgentTransport{
+		transport: &bearerAuthTransport{
+			transport: http.DefaultTransport,
+			token:     "test-token",
+		},
+		agent: "test-agent/1.0.0",
+	}
+
+	// Create an HTTP client with the transport chain
+	client := &http.Client{Transport: transport}
+
+	// Create a context with GraphQL features
+	ctx := github.WithGraphQLFeatures(context.Background(), "issues_copilot_assignment_api_support")
+
+	// Make a request with the context
+	req, err := http.NewRequestWithContext(ctx, "POST", testServer.URL, nil)
+	require.NoError(t, err)
+
+	resp, err := client.Do(req)
+	require.NoError(t, err)
+	defer resp.Body.Close()
+
+	// Verify all headers are set correctly
+	assert.Equal(t, "test-agent/1.0.0", capturedRequest.Header.Get("User-Agent"))
+	assert.Equal(t, "Bearer test-token", capturedRequest.Header.Get("Authorization"))
+	assert.Equal(t, "issues_copilot_assignment_api_support", capturedRequest.Header.Get("GraphQL-Features"))
+}
diff --git a/pkg/github/issues.go b/pkg/github/issues.go
index 63174c9e9..d6af14abb 100644
--- a/pkg/github/issues.go
+++ b/pkg/github/issues.go
@@ -1789,7 +1789,7 @@ func AssignCopilotToIssue(t translations.TranslationHelperFunc) inventory.Server
 
 			// Add the GraphQL-Features header for the agent assignment API
 			// The header will be read by the HTTP transport if it's configured to do so
-			ctxWithFeatures := withGraphQLFeatures(ctx, "issues_copilot_assignment_api_support")
+			ctxWithFeatures := WithGraphQLFeatures(ctx, "issues_copilot_assignment_api_support")
 
 			if err := client.Mutate(
 				ctxWithFeatures,
@@ -1917,8 +1917,8 @@ func AssignCodingAgentPrompt(t translations.TranslationHelperFunc) inventory.Ser
 // graphQLFeaturesKey is a context key for GraphQL feature flags
 type graphQLFeaturesKey struct{}
 
-// withGraphQLFeatures adds GraphQL feature flags to the context
-func withGraphQLFeatures(ctx context.Context, features ...string) context.Context {
+// WithGraphQLFeatures adds GraphQL feature flags to the context
+func WithGraphQLFeatures(ctx context.Context, features ...string) context.Context {
 	return context.WithValue(ctx, graphQLFeaturesKey{}, features)
 }