diff --git a/backend/internal/setup/setup.go b/backend/internal/setup/setup.go
index c10193faba..963926fa4e 100644
--- a/backend/internal/setup/setup.go
+++ b/backend/internal/setup/setup.go
@@ -495,10 +495,6 @@ func writeConfigFile(cfg *SetupConfig) error {
 			APIKeyPrefix    string  `yaml:"api_key_prefix"`
 			RateMultiplier  float64 `yaml:"rate_multiplier"`
 		} `yaml:"default"`
-		RateLimit struct {
-			RequestsPerMinute int `yaml:"requests_per_minute"`
-			BurstSize         int `yaml:"burst_size"`
-		} `yaml:"rate_limit"`
 		Timezone string `yaml:"timezone"`
 	}{
 		Server:   cfg.Server,
@@ -522,13 +518,6 @@ func writeConfigFile(cfg *SetupConfig) error {
 			APIKeyPrefix:    "sk-",
 			RateMultiplier:  1.0,
 		},
-		RateLimit: struct {
-			RequestsPerMinute int `yaml:"requests_per_minute"`
-			BurstSize         int `yaml:"burst_size"`
-		}{
-			RequestsPerMinute: 60,
-			BurstSize:         10,
-		},
 		Timezone: tz,
 	}
 
diff --git a/backend/internal/setup/setup_test.go b/backend/internal/setup/setup_test.go
index 71abebc0c9..7d4320ada0 100644
--- a/backend/internal/setup/setup_test.go
+++ b/backend/internal/setup/setup_test.go
@@ -11,6 +11,7 @@ import (
 
 	"github.com/DATA-DOG/go-sqlmock"
 	"github.com/lib/pq"
+	"gopkg.in/yaml.v3"
 )
 
 func TestDecideAdminBootstrap(t *testing.T) {
@@ -231,6 +232,48 @@ func TestWriteConfigFileIncludesRedisUsername(t *testing.T) {
 	}
 }
 
+func TestWriteConfigFileOmitsObsoleteRateLimit(t *testing.T) {
+	t.Setenv("DATA_DIR", t.TempDir())
+
+	if err := writeConfigFile(&SetupConfig{
+		Redis:    RedisConfig{Host: "redis", Port: 6379, Username: "app-user"},
+		Timezone: "UTC",
+	}); err != nil {
+		t.Fatalf("writeConfigFile() error = %v", err)
+	}
+
+	data, err := os.ReadFile(GetConfigFilePath())
+	if err != nil {
+		t.Fatalf("ReadFile() error = %v", err)
+	}
+	var config map[string]any
+	if err := yaml.Unmarshal(data, &config); err != nil {
+		t.Fatalf("generated config is invalid YAML: %v", err)
+	}
+	if rateLimit, exists := config["rate_limit"]; exists {
+		fields, ok := rateLimit.(map[string]any)
+		if !ok {
+			t.Fatalf("generated rate_limit must be a mapping: %#v", rateLimit)
+		}
+		for _, key := range []string{"requests_per_minute", "burst_size"} {
+			if _, present := fields[key]; present {
+				t.Fatalf("generated config contains obsolete rate_limit.%s: %s", key, data)
+			}
+		}
+	}
+	redis, ok := config["redis"].(map[string]any)
+	if !ok || redis["host"] != "redis" || redis["port"] != 6379 || redis["username"] != "app-user" {
+		t.Fatalf("generated config lost Redis settings: %#v", config["redis"])
+	}
+	if config["timezone"] != "UTC" {
+		t.Fatalf("generated config timezone = %#v, want UTC", config["timezone"])
+	}
+	defaults, ok := config["default"].(map[string]any)
+	if !ok || defaults["user_concurrency"] != defaultUserConcurrency || defaults["api_key_prefix"] != "sk-" {
+		t.Fatalf("generated config lost default settings: %#v", config["default"])
+	}
+}
+
 func TestDatabaseConnectionDSNsUseConfiguredTargetAndLegacyBootstrapDatabase(t *testing.T) {
 	cfg := &DatabaseConfig{
 		Host:     "db",