diff --git a/README.md b/README.md
index f169bd7..78dec73 100644
--- a/README.md
+++ b/README.md
@@ -939,6 +939,21 @@ Run multiple nanobot instances simultaneously with separate configs and runtime
 
 ### Quick Start
 
+**Initialize instances:**
+
+```bash
+# Create separate instance directories
+nanobot onboard --dir ~/.nanobot-telegram
+nanobot onboard --dir ~/.nanobot-discord
+nanobot onboard --dir ~/.nanobot-feishu
+```
+
+**Configure each instance:**
+
+Edit `~/.nanobot-telegram/config.json`, `~/.nanobot-discord/config.json`, etc. with different channel settings and workspaces.
+
+**Run instances:**
+
 ```bash
 # Instance A - Telegram bot
 nanobot gateway --config ~/.nanobot-telegram/config.json
@@ -1038,7 +1053,8 @@ nanobot gateway --config ~/.nanobot-telegram/config.json --workspace /tmp/nanobo
 
 | Command | Description |
 |---------|-------------|
-| `nanobot onboard` | Initialize config & workspace |
+| `nanobot onboard` | Initialize config & workspace at `~/.nanobot/` |
+| `nanobot onboard --dir <path>` | Initialize config & workspace at custom directory |
 | `nanobot agent -m "..."` | Chat with the agent |
 | `nanobot agent -w <workspace>` | Chat against a specific workspace |
 | `nanobot agent -w <workspace> -c <config>` | Chat against a specific workspace/config |
diff --git a/nanobot/cli/commands.py b/nanobot/cli/commands.py
index 2c8d6d3..def0144 100644
--- a/nanobot/cli/commands.py
+++ b/nanobot/cli/commands.py
@@ -168,43 +168,54 @@ def main(
 
 
 @app.command()
-def onboard():
+def onboard(
+    dir: str | None = typer.Option(None, "--dir", help="Base directory for config and workspace (default: ~/.nanobot/)"),
+):
     """Initialize nanobot configuration and workspace."""
-    from nanobot.config.loader import get_config_path, load_config, save_config
+    from nanobot.config.loader import load_config, save_config
     from nanobot.config.schema import Config
 
-    config_path = get_config_path()
+    # Determine base directory
+    if dir:
+        base_dir = Path(dir).expanduser().resolve()
+    else:
+        base_dir = Path.home() / ".nanobot"
 
+    config_path = base_dir / "config.json"
+    workspace_path = base_dir / "workspace"
+
+    # Ensure base directory exists
+    base_dir.mkdir(parents=True, exist_ok=True)
+
+    # Create or update config
     if config_path.exists():
         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 = Config()
-            save_config(config)
+            save_config(config, config_path)
             console.print(f"[green]✓[/green] Config reset to defaults at {config_path}")
         else:
-            config = load_config()
-            save_config(config)
+            config = load_config(config_path)
+            save_config(config, config_path)
             console.print(f"[green]✓[/green] Config refreshed at {config_path} (existing values preserved)")
     else:
-        save_config(Config())
+        save_config(Config(), config_path)
         console.print(f"[green]✓[/green] Created config at {config_path}")
 
     # Create workspace
-    workspace = get_workspace_path()
+    if not workspace_path.exists():
+        workspace_path.mkdir(parents=True, exist_ok=True)
+        console.print(f"[green]✓[/green] Created workspace at {workspace_path}")
 
-    if not workspace.exists():
-        workspace.mkdir(parents=True, exist_ok=True)
-        console.print(f"[green]✓[/green] Created workspace at {workspace}")
-
-    sync_workspace_templates(workspace)
+    sync_workspace_templates(workspace_path)
 
     console.print(f"\n{__logo__} nanobot is ready!")
     console.print("\nNext steps:")
-    console.print("  1. Add your API key to [cyan]~/.nanobot/config.json[/cyan]")
+    console.print(f"  1. Add your API key to [cyan]{config_path}[/cyan]")
     console.print("     Get one at: https://openrouter.ai/keys")
-    console.print("  2. Chat: [cyan]nanobot agent -m \"Hello!\"[/cyan]")
+    console.print(f"  2. Chat: [cyan]nanobot agent -m \"Hello!\" --config {config_path} --workspace {workspace_path}[/cyan]")
     console.print("\n[dim]Want Telegram/WhatsApp? See: https://github.com/HKUDS/nanobot#-chat-apps[/dim]")