diff --git a/cmd/ftl-controller/main.go b/cmd/ftl-controller/main.go
index 50059394d7..86601ca847 100644
--- a/cmd/ftl-controller/main.go
+++ b/cmd/ftl-controller/main.go
@@ -41,6 +41,7 @@ func main() {
 		kong.UsageOnError(),
 		kong.Vars{"version": ftl.Version, "timestamp": time.Unix(t, 0).Format(time.RFC3339)},
 	)
+	cli.ControllerConfig.SetDefaults()
 	ctx := log.ContextWithLogger(context.Background(), log.Configure(os.Stderr, cli.LogConfig))
 	err = observability.Init(ctx, "ftl-controller", ftl.Version, cli.ObservabilityConfig)
 	kctx.FatalIfErrorf(err, "failed to initialize observability")
diff --git a/cmd/ftl/cmd_box_run.go b/cmd/ftl/cmd_box_run.go
index 01528c8d4e..6197accdec 100644
--- a/cmd/ftl/cmd_box_run.go
+++ b/cmd/ftl/cmd_box_run.go
@@ -6,7 +6,6 @@ import (
 	"net/url"
 	"time"
 
-	"github.com/alecthomas/kong"
 	"github.com/jpillora/backoff"
 	"golang.org/x/sync/errgroup"
 
@@ -44,9 +43,7 @@ func (b *boxRunCmd) Run(ctx context.Context, projConfig projectconfig.Config) er
 		Key:         model.NewLocalControllerKey(0),
 		DSN:         b.DSN,
 	}
-	if err := kong.ApplyDefaults(&config); err != nil {
-		return err
-	}
+	config.SetDefaults()
 
 	// Start the controller.
 	runnerPortAllocator, err := bind.NewBindAllocator(b.RunnerBase)
diff --git a/cmd/ftl/cmd_serve.go b/cmd/ftl/cmd_serve.go
index 1f985915fe..117712cd0a 100644
--- a/cmd/ftl/cmd_serve.go
+++ b/cmd/ftl/cmd_serve.go
@@ -14,7 +14,6 @@ import (
 	"time"
 
 	"connectrpc.com/connect"
-	"github.com/alecthomas/kong"
 	"github.com/alecthomas/types/optional"
 	"golang.org/x/sync/errgroup"
 
@@ -124,9 +123,7 @@ func (s *serveCmd) run(ctx context.Context, projConfig projectconfig.Config, ini
 			Key:          model.NewLocalControllerKey(i),
 			DSN:          dsn,
 		}
-		if err := kong.ApplyDefaults(&config); err != nil {
-			return err
-		}
+		config.SetDefaults()
 		config.ModuleUpdateFrequency = time.Second * 1
 
 		scope := fmt.Sprintf("controller%d", i)