diff --git a/pkg/http/middleware/request_config.go b/pkg/http/middleware/request_config.go
index 6102825192..2c14edaa5c 100644
--- a/pkg/http/middleware/request_config.go
+++ b/pkg/http/middleware/request_config.go
@@ -26,12 +26,12 @@ func WithRequestConfig(next http.Handler) http.Handler {
 		}
 
 		// Toolsets
-		if toolsets := headers.ParseCommaSeparated(r.Header.Get(headers.MCPToolsetsHeader)); len(toolsets) > 0 {
+		if toolsets := headers.ParseCommaSeparated(strings.Join(r.Header.Values(headers.MCPToolsetsHeader), ",")); len(toolsets) > 0 {
 			ctx = ghcontext.WithToolsets(ctx, toolsets)
 		}
 
 		// Tools
-		if tools := headers.ParseCommaSeparated(r.Header.Get(headers.MCPToolsHeader)); len(tools) > 0 {
+		if tools := headers.ParseCommaSeparated(strings.Join(r.Header.Values(headers.MCPToolsHeader), ",")); len(tools) > 0 {
 			ctx = ghcontext.WithTools(ctx, tools)
 		}
 
@@ -41,7 +41,7 @@ func WithRequestConfig(next http.Handler) http.Handler {
 		}
 
 		// Excluded tools
-		if excludeTools := headers.ParseCommaSeparated(r.Header.Get(headers.MCPExcludeToolsHeader)); len(excludeTools) > 0 {
+		if excludeTools := headers.ParseCommaSeparated(strings.Join(r.Header.Values(headers.MCPExcludeToolsHeader), ",")); len(excludeTools) > 0 {
 			ctx = ghcontext.WithExcludeTools(ctx, excludeTools)
 		}
 
@@ -54,7 +54,7 @@ func WithRequestConfig(next http.Handler) http.Handler {
 		_, hasHeaderFeatures := r.Header[http.CanonicalHeaderKey(headers.MCPFeaturesHeader)]
 		_, hasQueryFeatures := query[queryParamFeatures]
 		if hasHeaderFeatures {
-			ctx = ghcontext.WithHeaderFeatures(ctx, headers.ParseCommaSeparated(r.Header.Get(headers.MCPFeaturesHeader)))
+			ctx = ghcontext.WithHeaderFeatures(ctx, headers.ParseCommaSeparated(strings.Join(r.Header.Values(headers.MCPFeaturesHeader), ",")))
 		} else if hasQueryFeatures {
 			ctx = ghcontext.WithHeaderFeatures(ctx, headers.ParseCommaSeparated(query.Get(queryParamFeatures)))
 		}
diff --git a/pkg/http/middleware/request_config_test.go b/pkg/http/middleware/request_config_test.go
index 1937d0986b..ce572d5084 100644
--- a/pkg/http/middleware/request_config_test.go
+++ b/pkg/http/middleware/request_config_test.go
@@ -1,6 +1,7 @@
 package middleware
 
 import (
+	"context"
 	"net/http"
 	"net/http/httptest"
 	"testing"
@@ -10,6 +11,30 @@ import (
 	"github.com/stretchr/testify/assert"
 )
 
+func TestWithRequestConfigRepeatedListHeaders(t *testing.T) {
+	tests := []struct {
+		name   string
+		header string
+		get    func(context.Context) []string
+	}{
+		{"toolsets", headers.MCPToolsetsHeader, ghcontext.GetToolsets},
+		{"tools", headers.MCPToolsHeader, ghcontext.GetTools},
+		{"excluded tools", headers.MCPExcludeToolsHeader, ghcontext.GetExcludeTools},
+		{"features", headers.MCPFeaturesHeader, ghcontext.GetHeaderFeatures},
+	}
+	for _, tc := range tests {
+		t.Run(tc.name, func(t *testing.T) {
+			req := httptest.NewRequest(http.MethodGet, "/?features=query_flag", nil)
+			req.Header.Add(tc.header, "first, second")
+			req.Header.Add(tc.header, " third, , fourth ")
+			handler := WithRequestConfig(http.HandlerFunc(func(_ http.ResponseWriter, r *http.Request) {
+				assert.Equal(t, []string{"first", "second", "third", "fourth"}, tc.get(r.Context()))
+			}))
+			handler.ServeHTTP(httptest.NewRecorder(), req)
+		})
+	}
+}
+
 func TestWithRequestConfigFeatureSelection(t *testing.T) {
 	tests := []struct {
 		name         string