diff --git a/nanobot/cli/commands.py b/nanobot/cli/commands.py
index 4ed4f314..18e0977f 100644
--- a/nanobot/cli/commands.py
+++ b/nanobot/cli/commands.py
@@ -597,11 +597,7 @@ def onboard(
     workspace: str | None = typer.Option(None, "--workspace", "-w", help="Workspace directory"),
     config: str | None = typer.Option(None, "--config", "-c", help="Path to config file"),
     wizard: bool = typer.Option(False, "--wizard", help="Use interactive wizard"),
-    refresh: bool = typer.Option(
-        False,
-        "--refresh",
-        help="Refresh config, preserving existing settings without prompting",
-    ),
+    non_interactive_refresh: bool = typer.Option(False, "--refresh", help="Refresh config, preserving existing settings without prompting"),
 ):
     """Initialize nanobot configuration and workspace."""
     from nanobot.config.loader import get_config_path, load_config, save_config, set_config_path
@@ -623,25 +619,24 @@ def onboard(
     if config_path.exists():
         if wizard:
             config = _apply_workspace_override(load_config(config_path))
-        elif refresh:
-            config = _apply_workspace_override(load_config(config_path))
-            save_config(config, config_path)
-            console.print(
-                f"[green]✓[/green] Config refreshed at {config_path} (existing values preserved)"
-            )
         else:
-            console.print(f"[yellow]Config already exists at {config_path}[/yellow]")
-            console.print(
-                "  [bold]y[/bold] = overwrite with defaults (existing values will be lost)"
-            )
-            console.print(
-                "  [bold]N[/bold] = refresh config, keeping existing values and adding new fields"
-            )
-            if typer.confirm("Overwrite?"):
-                config = _apply_workspace_override(Config())
-                save_config(config, config_path)
-                console.print(f"[green]✓[/green] Config reset to defaults at {config_path}")
-            else:
+            should_refresh = non_interactive_refresh
+            if not non_interactive_refresh:
+                console.print(f"[yellow]Config already exists at {config_path}[/yellow]")
+                console.print(
+                    "  [bold]y[/bold] = overwrite with defaults (existing values will be lost)"
+                )
+                console.print(
+                    "  [bold]N[/bold] = refresh config, keeping existing values and adding new fields"
+                )
+                if typer.confirm("Overwrite?"):
+                    config = _apply_workspace_override(Config())
+                    save_config(config, config_path)
+                    console.print(f"[green]✓[/green] Config reset to defaults at {config_path}")
+                else:
+                    should_refresh = True
+
+            if should_refresh:
                 config = _apply_workspace_override(load_config(config_path))
                 save_config(config, config_path)
                 console.print(