diff --git a/README.md b/README.md
index 18770dc..5bd11f8 100644
--- a/README.md
+++ b/README.md
@@ -905,30 +905,92 @@ MCP tools are automatically discovered and registered on startup. The LLM can us
 
 ## Multiple Instances
 
-Run multiple nanobot instances simultaneously, each with its own workspace and configuration.
+Run multiple nanobot instances simultaneously with separate configs and runtime data. Use `--config` as the main entrypoint, and optionally use `--workspace` to override the workspace for a specific run.
+
+### Quick Start
 
 ```bash
 # Instance A - Telegram bot
-nanobot gateway -w ~/.nanobot/botA -p 18791
+nanobot gateway --config ~/.nanobot-telegram/config.json
 
-# Instance B - Discord bot
-nanobot gateway -w ~/.nanobot/botB -p 18792
+# Instance B - Discord bot  
+nanobot gateway --config ~/.nanobot-discord/config.json
 
-# Instance C - Using custom config file
-nanobot gateway -w ~/.nanobot/botC -c ~/.nanobot/botC/config.json -p 18793
+# Instance C - Feishu bot with custom port
+nanobot gateway --config ~/.nanobot-feishu/config.json --port 18792
 ```
 
-| Option | Short | Description |
-|--------|-------|-------------|
-| `--workspace` | `-w` | Workspace directory (default: `~/.nanobot/workspace`) |
-| `--config` | `-c` | Config file path (default: `~/.nanobot/config.json`) |
-| `--port` | `-p` | Gateway port (default: `18790`) |
+### Path Resolution
 
-Each instance has its own:
-- Workspace directory (MEMORY.md, HEARTBEAT.md, session files)
-- Cron jobs storage (`workspace/cron/jobs.json`)
-- Configuration (if using `--config`)
+When using `--config`, nanobot derives its runtime data directory from the config file location. The workspace still comes from `agents.defaults.workspace` unless you override it with `--workspace`.
 
+| Component | Resolved From | Example |
+|-----------|---------------|---------|
+| **Config** | `--config` path | `~/.nanobot-A/config.json` |
+| **Workspace** | `--workspace` or config | `~/.nanobot-A/workspace/` |
+| **Cron Jobs** | config directory | `~/.nanobot-A/cron/` |
+| **Media / runtime state** | config directory | `~/.nanobot-A/media/` |
+
+### How It Works
+
+- `--config` selects which config file to load
+- By default, the workspace comes from `agents.defaults.workspace` in that config
+- If you pass `--workspace`, it overrides the workspace from the config file
+
+### Minimal Setup
+
+1. Copy your base config into a new instance directory.
+2. Set a different `agents.defaults.workspace` for that instance.
+3. Start the instance with `--config`.
+
+Example config:
+
+```json
+{
+  "agents": {
+    "defaults": {
+      "workspace": "~/.nanobot-telegram/workspace",
+      "model": "anthropic/claude-sonnet-4-6"
+    }
+  },
+  "channels": {
+    "telegram": {
+      "enabled": true,
+      "token": "YOUR_TELEGRAM_BOT_TOKEN"
+    }
+  },
+  "gateway": {
+    "port": 18790
+  }
+}
+```
+
+Start separate instances:
+
+```bash
+nanobot gateway --config ~/.nanobot-telegram/config.json
+nanobot gateway --config ~/.nanobot-discord/config.json
+```
+
+Override workspace for one-off runs when needed:
+
+```bash
+nanobot gateway --config ~/.nanobot-telegram/config.json --workspace /tmp/nanobot-telegram-test
+```
+
+### Common Use Cases
+
+- Run separate bots for Telegram, Discord, Feishu, and other platforms
+- Keep testing and production instances isolated
+- Use different models or providers for different teams
+- Serve multiple tenants with separate configs and runtime data
+
+### Notes
+
+- Each instance must use a different port if they run at the same time
+- Use a different workspace per instance if you want isolated memory, sessions, and skills
+- `--workspace` overrides the workspace defined in the config file
+- Cron jobs and runtime media/state are derived from the config directory
 
 ## CLI Reference
 
diff --git a/bridge/src/whatsapp.ts b/bridge/src/whatsapp.ts
index b91bacc..f0485bd 100644
--- a/bridge/src/whatsapp.ts
+++ b/bridge/src/whatsapp.ts
@@ -18,7 +18,6 @@ import qrcode from 'qrcode-terminal';
 import pino from 'pino';
 import { writeFile, mkdir } from 'fs/promises';
 import { join } from 'path';
-import { homedir } from 'os';
 import { randomBytes } from 'crypto';
 
 const VERSION = '0.1.0';
@@ -162,7 +161,7 @@ export class WhatsAppClient {
 
   private async downloadMedia(msg: any, mimetype?: string, fileName?: string): Promise<string | null> {
     try {
-      const mediaDir = join(homedir(), '.nanobot', 'media');
+      const mediaDir = join(this.options.authDir, '..', 'media');
       await mkdir(mediaDir, { recursive: true });
 
       const buffer = await downloadMediaMessage(msg, 'buffer', {}) as Buffer;
diff --git a/nanobot/channels/discord.py b/nanobot/channels/discord.py
index 0187c62..2ee4f77 100644
--- a/nanobot/channels/discord.py
+++ b/nanobot/channels/discord.py
@@ -12,6 +12,7 @@ from loguru import logger
 from nanobot.bus.events import OutboundMessage
 from nanobot.bus.queue import MessageBus
 from nanobot.channels.base import BaseChannel
+from nanobot.config.paths import get_media_dir
 from nanobot.config.schema import DiscordConfig
 from nanobot.utils.helpers import split_message
 
@@ -289,7 +290,7 @@ class DiscordChannel(BaseChannel):
 
         content_parts = [content] if content else []
         media_paths: list[str] = []
-        media_dir = Path.home() / ".nanobot" / "media"
+        media_dir = get_media_dir("discord")
 
         for attachment in payload.get("attachments") or []:
             url = attachment.get("url")
diff --git a/nanobot/channels/feishu.py b/nanobot/channels/feishu.py
index 2dcf710..a637025 100644
--- a/nanobot/channels/feishu.py
+++ b/nanobot/channels/feishu.py
@@ -14,6 +14,7 @@ from loguru import logger
 from nanobot.bus.events import OutboundMessage
 from nanobot.bus.queue import MessageBus
 from nanobot.channels.base import BaseChannel
+from nanobot.config.paths import get_media_dir
 from nanobot.config.schema import FeishuConfig
 
 import importlib.util
@@ -732,8 +733,7 @@ class FeishuChannel(BaseChannel):
             (file_path, content_text) - file_path is None if download failed
         """
         loop = asyncio.get_running_loop()
-        media_dir = Path.home() / ".nanobot" / "media"
-        media_dir.mkdir(parents=True, exist_ok=True)
+        media_dir = get_media_dir("feishu")
 
         data, filename = None, None
 
diff --git a/nanobot/channels/matrix.py b/nanobot/channels/matrix.py
index 4967ac1..63cb0ca 100644
--- a/nanobot/channels/matrix.py
+++ b/nanobot/channels/matrix.py
@@ -38,7 +38,7 @@ except ImportError as e:
 
 from nanobot.bus.events import OutboundMessage
 from nanobot.channels.base import BaseChannel
-from nanobot.config.loader import get_data_dir
+from nanobot.config.paths import get_data_dir, get_media_dir
 from nanobot.utils.helpers import safe_filename
 
 TYPING_NOTICE_TIMEOUT_MS = 30_000
@@ -490,9 +490,7 @@ class MatrixChannel(BaseChannel):
         return False
 
     def _media_dir(self) -> Path:
-        d = get_data_dir() / "media" / "matrix"
-        d.mkdir(parents=True, exist_ok=True)
-        return d
+        return get_media_dir("matrix")
 
     @staticmethod
     def _event_source_content(event: RoomMessage) -> dict[str, Any]:
diff --git a/nanobot/channels/mochat.py b/nanobot/channels/mochat.py
index e762dfd..09e31c3 100644
--- a/nanobot/channels/mochat.py
+++ b/nanobot/channels/mochat.py
@@ -15,8 +15,8 @@ from loguru import logger
 from nanobot.bus.events import OutboundMessage
 from nanobot.bus.queue import MessageBus
 from nanobot.channels.base import BaseChannel
+from nanobot.config.paths import get_runtime_subdir
 from nanobot.config.schema import MochatConfig
-from nanobot.utils.helpers import get_data_path
 
 try:
     import socketio
@@ -224,7 +224,7 @@ class MochatChannel(BaseChannel):
         self._socket: Any = None
         self._ws_connected = self._ws_ready = False
 
-        self._state_dir = get_data_path() / "mochat"
+        self._state_dir = get_runtime_subdir("mochat")
         self._cursor_path = self._state_dir / "session_cursors.json"
         self._session_cursor: dict[str, int] = {}
         self._cursor_save_task: asyncio.Task | None = None
diff --git a/nanobot/channels/telegram.py b/nanobot/channels/telegram.py
index 501a3c1..ecb1440 100644
--- a/nanobot/channels/telegram.py
+++ b/nanobot/channels/telegram.py
@@ -15,6 +15,7 @@ from telegram.request import HTTPXRequest
 from nanobot.bus.events import OutboundMessage
 from nanobot.bus.queue import MessageBus
 from nanobot.channels.base import BaseChannel
+from nanobot.config.paths import get_media_dir
 from nanobot.config.schema import TelegramConfig
 from nanobot.utils.helpers import split_message
 
@@ -536,10 +537,7 @@ class TelegramChannel(BaseChannel):
                     getattr(media_file, 'mime_type', None),
                     getattr(media_file, 'file_name', None),
                 )
-                # Save to workspace/media/
-                from pathlib import Path
-                media_dir = Path.home() / ".nanobot" / "media"
-                media_dir.mkdir(parents=True, exist_ok=True)
+                media_dir = get_media_dir("telegram")
 
                 file_path = media_dir / f"{media_file.file_id[:16]}{ext}"
                 await file.download_to_drive(str(file_path))
diff --git a/nanobot/cli/commands.py b/nanobot/cli/commands.py
index ca5d8d7..da8906d 100644
--- a/nanobot/cli/commands.py
+++ b/nanobot/cli/commands.py
@@ -30,6 +30,7 @@ from rich.table import Table
 from rich.text import Text
 
 from nanobot import __logo__, __version__
+from nanobot.config.paths import get_workspace_path
 from nanobot.config.schema import Config
 from nanobot.utils.helpers import sync_workspace_templates
 
@@ -99,7 +100,9 @@ def _init_prompt_session() -> None:
     except Exception:
         pass
 
-    history_file = Path.home() / ".nanobot" / "history" / "cli_history"
+    from nanobot.config.paths import get_cli_history_path
+
+    history_file = get_cli_history_path()
     history_file.parent.mkdir(parents=True, exist_ok=True)
 
     _PROMPT_SESSION = PromptSession(
@@ -170,7 +173,6 @@ def onboard():
     """Initialize nanobot configuration and workspace."""
     from nanobot.config.loader import get_config_path, load_config, save_config
     from nanobot.config.schema import Config
-    from nanobot.utils.helpers import get_workspace_path
 
     config_path = get_config_path()
 
@@ -272,14 +274,25 @@ def _make_provider(config: Config):
 def gateway(
     port: int = typer.Option(18790, "--port", "-p", help="Gateway port"),
     workspace: str | None = typer.Option(None, "--workspace", "-w", help="Workspace directory"),
-    config: str | None = typer.Option(None, "--config", "-c", help="Config file path"),
     verbose: bool = typer.Option(False, "--verbose", "-v", help="Verbose output"),
+    config: str | None = typer.Option(None, "--config", "-c", help="Path to config file"),
 ):
     """Start the nanobot gateway."""
+    # Set config path if provided (must be done before any imports that use get_data_dir)
+    if config:
+        from nanobot.config.loader import set_config_path
+        config_path = Path(config).expanduser().resolve()
+        if not config_path.exists():
+            console.print(f"[red]Error: Config file not found: {config_path}[/red]")
+            raise typer.Exit(1)
+        set_config_path(config_path)
+        console.print(f"[dim]Using config: {config_path}[/dim]")
+    
     from nanobot.agent.loop import AgentLoop
     from nanobot.bus.queue import MessageBus
     from nanobot.channels.manager import ChannelManager
     from nanobot.config.loader import load_config
+    from nanobot.config.paths import get_cron_dir
     from nanobot.cron.service import CronService
     from nanobot.cron.types import CronJob
     from nanobot.heartbeat.service import HeartbeatService
@@ -289,20 +302,18 @@ def gateway(
         import logging
         logging.basicConfig(level=logging.DEBUG)
 
-    config_path = Path(config) if config else None
-    config = load_config(config_path)
+    console.print(f"{__logo__} Starting nanobot gateway on port {port}...")
+
+    config = load_config()
     if workspace:
         config.agents.defaults.workspace = workspace
-
-    console.print(f"{__logo__} Starting nanobot gateway on port {port}...")
     sync_workspace_templates(config.workspace_path)
     bus = MessageBus()
     provider = _make_provider(config)
     session_manager = SessionManager(config.workspace_path)
 
     # Create cron service first (callback set after agent creation)
-    # Use workspace path for per-instance cron store
-    cron_store_path = config.workspace_path / "cron" / "jobs.json"
+    cron_store_path = get_cron_dir() / "jobs.json"
     cron = CronService(cron_store_path)
 
     # Create agent with cron service
@@ -471,7 +482,8 @@ def agent(
 
     from nanobot.agent.loop import AgentLoop
     from nanobot.bus.queue import MessageBus
-    from nanobot.config.loader import get_data_dir, load_config
+    from nanobot.config.loader import load_config
+    from nanobot.config.paths import get_cron_dir
     from nanobot.cron.service import CronService
 
     config = load_config()
@@ -481,7 +493,7 @@ def agent(
     provider = _make_provider(config)
 
     # Create cron service for tool usage (no callback needed for CLI unless running)
-    cron_store_path = get_data_dir() / "cron" / "jobs.json"
+    cron_store_path = get_cron_dir() / "jobs.json"
     cron = CronService(cron_store_path)
 
     if logs:
@@ -747,7 +759,9 @@ def _get_bridge_dir() -> Path:
     import subprocess
 
     # User's bridge location
-    user_bridge = Path.home() / ".nanobot" / "bridge"
+    from nanobot.config.paths import get_bridge_install_dir
+
+    user_bridge = get_bridge_install_dir()
 
     # Check if already built
     if (user_bridge / "dist" / "index.js").exists():
@@ -805,6 +819,7 @@ def channels_login():
     import subprocess
 
     from nanobot.config.loader import load_config
+    from nanobot.config.paths import get_runtime_subdir
 
     config = load_config()
     bridge_dir = _get_bridge_dir()
@@ -815,6 +830,7 @@ def channels_login():
     env = {**os.environ}
     if config.channels.whatsapp.bridge_token:
         env["BRIDGE_TOKEN"] = config.channels.whatsapp.bridge_token
+    env["AUTH_DIR"] = str(get_runtime_subdir("whatsapp-auth"))
 
     try:
         subprocess.run(["npm", "start"], cwd=bridge_dir, check=True, env=env)
diff --git a/nanobot/config/__init__.py b/nanobot/config/__init__.py
index 6c59668..e2c24f8 100644
--- a/nanobot/config/__init__.py
+++ b/nanobot/config/__init__.py
@@ -1,6 +1,30 @@
 """Configuration module for nanobot."""
 
 from nanobot.config.loader import get_config_path, load_config
+from nanobot.config.paths import (
+    get_bridge_install_dir,
+    get_cli_history_path,
+    get_cron_dir,
+    get_data_dir,
+    get_legacy_sessions_dir,
+    get_logs_dir,
+    get_media_dir,
+    get_runtime_subdir,
+    get_workspace_path,
+)
 from nanobot.config.schema import Config
 
-__all__ = ["Config", "load_config", "get_config_path"]
+__all__ = [
+    "Config",
+    "load_config",
+    "get_config_path",
+    "get_data_dir",
+    "get_runtime_subdir",
+    "get_media_dir",
+    "get_cron_dir",
+    "get_logs_dir",
+    "get_workspace_path",
+    "get_cli_history_path",
+    "get_bridge_install_dir",
+    "get_legacy_sessions_dir",
+]
diff --git a/nanobot/config/loader.py b/nanobot/config/loader.py
index c789efd..7d309e5 100644
--- a/nanobot/config/loader.py
+++ b/nanobot/config/loader.py
@@ -6,17 +6,23 @@ from pathlib import Path
 from nanobot.config.schema import Config
 
 
+# Global variable to store current config path (for multi-instance support)
+_current_config_path: Path | None = None
+
+
+def set_config_path(path: Path) -> None:
+    """Set the current config path (used to derive data directory)."""
+    global _current_config_path
+    _current_config_path = path
+
+
 def get_config_path() -> Path:
-    """Get the default configuration file path."""
+    """Get the configuration file path."""
+    if _current_config_path:
+        return _current_config_path
     return Path.home() / ".nanobot" / "config.json"
 
 
-def get_data_dir() -> Path:
-    """Get the nanobot data directory."""
-    from nanobot.utils.helpers import get_data_path
-    return get_data_path()
-
-
 def load_config(config_path: Path | None = None) -> Config:
     """
     Load configuration from file or create default.
diff --git a/nanobot/config/paths.py b/nanobot/config/paths.py
new file mode 100644
index 0000000..f4dfbd9
--- /dev/null
+++ b/nanobot/config/paths.py
@@ -0,0 +1,55 @@
+"""Runtime path helpers derived from the active config context."""
+
+from __future__ import annotations
+
+from pathlib import Path
+
+from nanobot.config.loader import get_config_path
+from nanobot.utils.helpers import ensure_dir
+
+
+def get_data_dir() -> Path:
+    """Return the instance-level runtime data directory."""
+    return ensure_dir(get_config_path().parent)
+
+
+def get_runtime_subdir(name: str) -> Path:
+    """Return a named runtime subdirectory under the instance data dir."""
+    return ensure_dir(get_data_dir() / name)
+
+
+def get_media_dir(channel: str | None = None) -> Path:
+    """Return the media directory, optionally namespaced per channel."""
+    base = get_runtime_subdir("media")
+    return ensure_dir(base / channel) if channel else base
+
+
+def get_cron_dir() -> Path:
+    """Return the cron storage directory."""
+    return get_runtime_subdir("cron")
+
+
+def get_logs_dir() -> Path:
+    """Return the logs directory."""
+    return get_runtime_subdir("logs")
+
+
+def get_workspace_path(workspace: str | None = None) -> Path:
+    """Resolve and ensure the agent workspace path."""
+    path = Path(workspace).expanduser() if workspace else Path.home() / ".nanobot" / "workspace"
+    return ensure_dir(path)
+
+
+def get_cli_history_path() -> Path:
+    """Return the shared CLI history file path."""
+    return Path.home() / ".nanobot" / "history" / "cli_history"
+
+
+def get_bridge_install_dir() -> Path:
+    """Return the shared WhatsApp bridge installation directory."""
+    return Path.home() / ".nanobot" / "bridge"
+
+
+def get_legacy_sessions_dir() -> Path:
+    """Return the legacy global session directory used for migration fallback."""
+    return Path.home() / ".nanobot" / "sessions"
diff --git a/nanobot/session/manager.py b/nanobot/session/manager.py
index dce4b2e..f0a6484 100644
--- a/nanobot/session/manager.py
+++ b/nanobot/session/manager.py
@@ -9,6 +9,7 @@ from typing import Any
 
 from loguru import logger
 
+from nanobot.config.paths import get_legacy_sessions_dir
 from nanobot.utils.helpers import ensure_dir, safe_filename
 
 
@@ -79,7 +80,7 @@ class SessionManager:
     def __init__(self, workspace: Path):
         self.workspace = workspace
         self.sessions_dir = ensure_dir(self.workspace / "sessions")
-        self.legacy_sessions_dir = Path.home() / ".nanobot" / "sessions"
+        self.legacy_sessions_dir = get_legacy_sessions_dir()
         self._cache: dict[str, Session] = {}
 
     def _get_session_path(self, key: str) -> Path:
diff --git a/nanobot/utils/__init__.py b/nanobot/utils/__init__.py
index 9163e38..46f02ac 100644
--- a/nanobot/utils/__init__.py
+++ b/nanobot/utils/__init__.py
@@ -1,5 +1,5 @@
 """Utility functions for nanobot."""
 
-from nanobot.utils.helpers import ensure_dir, get_data_path, get_workspace_path
+from nanobot.utils.helpers import ensure_dir
 
-__all__ = ["ensure_dir", "get_workspace_path", "get_data_path"]
+__all__ = ["ensure_dir"]
diff --git a/nanobot/utils/helpers.py b/nanobot/utils/helpers.py
index c57c365..57c60dc 100644
--- a/nanobot/utils/helpers.py
+++ b/nanobot/utils/helpers.py
@@ -24,17 +24,6 @@ def ensure_dir(path: Path) -> Path:
     return path
 
 
-def get_data_path() -> Path:
-    """~/.nanobot data directory."""
-    return ensure_dir(Path.home() / ".nanobot")
-
-
-def get_workspace_path(workspace: str | None = None) -> Path:
-    """Resolve and ensure workspace path. Defaults to ~/.nanobot/workspace."""
-    path = Path(workspace).expanduser() if workspace else Path.home() / ".nanobot" / "workspace"
-    return ensure_dir(path)
-
-
 def timestamp() -> str:
     """Current ISO timestamp."""
     return datetime.now().isoformat()
diff --git a/tests/test_commands.py b/tests/test_commands.py
index 044d113..a276653 100644
--- a/tests/test_commands.py
+++ b/tests/test_commands.py
@@ -14,13 +14,17 @@ from nanobot.providers.registry import find_by_model
 runner = CliRunner()
 
 
+class _StopGateway(RuntimeError):
+    pass
+
+
 @pytest.fixture
 def mock_paths():
     """Mock config/workspace paths for test isolation."""
     with patch("nanobot.config.loader.get_config_path") as mock_cp, \
          patch("nanobot.config.loader.save_config") as mock_sc, \
          patch("nanobot.config.loader.load_config") as mock_lc, \
-         patch("nanobot.utils.helpers.get_workspace_path") as mock_ws:
+         patch("nanobot.cli.commands.get_workspace_path") as mock_ws:
 
         base_dir = Path("./test_onboard_data")
         if base_dir.exists():
@@ -128,3 +132,94 @@ def test_litellm_provider_canonicalizes_github_copilot_hyphen_prefix():
 def test_openai_codex_strip_prefix_supports_hyphen_and_underscore():
     assert _strip_model_prefix("openai-codex/gpt-5.1-codex") == "gpt-5.1-codex"
     assert _strip_model_prefix("openai_codex/gpt-5.1-codex") == "gpt-5.1-codex"
+
+
+def test_gateway_uses_workspace_from_config_by_default(monkeypatch, tmp_path: Path) -> None:
+    config_file = tmp_path / "instance" / "config.json"
+    config_file.parent.mkdir(parents=True)
+    config_file.write_text("{}")
+
+    config = Config()
+    config.agents.defaults.workspace = str(tmp_path / "config-workspace")
+    seen: dict[str, Path] = {}
+
+    monkeypatch.setattr(
+        "nanobot.config.loader.set_config_path",
+        lambda path: seen.__setitem__("config_path", path),
+    )
+    monkeypatch.setattr("nanobot.config.loader.load_config", lambda: config)
+    monkeypatch.setattr(
+        "nanobot.cli.commands.sync_workspace_templates",
+        lambda path: seen.__setitem__("workspace", path),
+    )
+    monkeypatch.setattr(
+        "nanobot.cli.commands._make_provider",
+        lambda _config: (_ for _ in ()).throw(_StopGateway("stop")),
+    )
+
+    result = runner.invoke(app, ["gateway", "--config", str(config_file)])
+
+    assert isinstance(result.exception, _StopGateway)
+    assert seen["config_path"] == config_file.resolve()
+    assert seen["workspace"] == Path(config.agents.defaults.workspace)
+
+
+def test_gateway_workspace_option_overrides_config(monkeypatch, tmp_path: Path) -> None:
+    config_file = tmp_path / "instance" / "config.json"
+    config_file.parent.mkdir(parents=True)
+    config_file.write_text("{}")
+
+    config = Config()
+    config.agents.defaults.workspace = str(tmp_path / "config-workspace")
+    override = tmp_path / "override-workspace"
+    seen: dict[str, Path] = {}
+
+    monkeypatch.setattr("nanobot.config.loader.set_config_path", lambda _path: None)
+    monkeypatch.setattr("nanobot.config.loader.load_config", lambda: config)
+    monkeypatch.setattr(
+        "nanobot.cli.commands.sync_workspace_templates",
+        lambda path: seen.__setitem__("workspace", path),
+    )
+    monkeypatch.setattr(
+        "nanobot.cli.commands._make_provider",
+        lambda _config: (_ for _ in ()).throw(_StopGateway("stop")),
+    )
+
+    result = runner.invoke(
+        app,
+        ["gateway", "--config", str(config_file), "--workspace", str(override)],
+    )
+
+    assert isinstance(result.exception, _StopGateway)
+    assert seen["workspace"] == override
+    assert config.workspace_path == override
+
+
+def test_gateway_uses_config_directory_for_cron_store(monkeypatch, tmp_path: Path) -> None:
+    config_file = tmp_path / "instance" / "config.json"
+    config_file.parent.mkdir(parents=True)
+    config_file.write_text("{}")
+
+    config = Config()
+    config.agents.defaults.workspace = str(tmp_path / "config-workspace")
+    seen: dict[str, Path] = {}
+
+    monkeypatch.setattr("nanobot.config.loader.set_config_path", lambda _path: None)
+    monkeypatch.setattr("nanobot.config.loader.load_config", lambda: config)
+    monkeypatch.setattr("nanobot.config.paths.get_cron_dir", lambda: config_file.parent / "cron")
+    monkeypatch.setattr("nanobot.cli.commands.sync_workspace_templates", lambda _path: None)
+    monkeypatch.setattr("nanobot.cli.commands._make_provider", lambda _config: object())
+    monkeypatch.setattr("nanobot.bus.queue.MessageBus", lambda: object())
+    monkeypatch.setattr("nanobot.session.manager.SessionManager", lambda _workspace: object())
+
+    class _StopCron:
+        def __init__(self, store_path: Path) -> None:
+            seen["cron_store"] = store_path
+            raise _StopGateway("stop")
+
+    monkeypatch.setattr("nanobot.cron.service.CronService", _StopCron)
+
+    result = runner.invoke(app, ["gateway", "--config", str(config_file)])
+
+    assert isinstance(result.exception, _StopGateway)
+    assert seen["cron_store"] == config_file.parent / "cron" / "jobs.json"
diff --git a/tests/test_config_paths.py b/tests/test_config_paths.py
new file mode 100644
index 0000000..473a6c8
--- /dev/null
+++ b/tests/test_config_paths.py
@@ -0,0 +1,42 @@
+from pathlib import Path
+
+from nanobot.config.paths import (
+    get_bridge_install_dir,
+    get_cli_history_path,
+    get_cron_dir,
+    get_data_dir,
+    get_legacy_sessions_dir,
+    get_logs_dir,
+    get_media_dir,
+    get_runtime_subdir,
+    get_workspace_path,
+)
+
+
+def test_runtime_dirs_follow_config_path(monkeypatch, tmp_path: Path) -> None:
+    config_file = tmp_path / "instance-a" / "config.json"
+    monkeypatch.setattr("nanobot.config.paths.get_config_path", lambda: config_file)
+
+    assert get_data_dir() == config_file.parent
+    assert get_runtime_subdir("cron") == config_file.parent / "cron"
+    assert get_cron_dir() == config_file.parent / "cron"
+    assert get_logs_dir() == config_file.parent / "logs"
+
+
+def test_media_dir_supports_channel_namespace(monkeypatch, tmp_path: Path) -> None:
+    config_file = tmp_path / "instance-b" / "config.json"
+    monkeypatch.setattr("nanobot.config.paths.get_config_path", lambda: config_file)
+
+    assert get_media_dir() == config_file.parent / "media"
+    assert get_media_dir("telegram") == config_file.parent / "media" / "telegram"
+
+
+def test_shared_and_legacy_paths_remain_global() -> None:
+    assert get_cli_history_path() == Path.home() / ".nanobot" / "history" / "cli_history"
+    assert get_bridge_install_dir() == Path.home() / ".nanobot" / "bridge"
+    assert get_legacy_sessions_dir() == Path.home() / ".nanobot" / "sessions"
+
+
+def test_workspace_path_is_explicitly_resolved() -> None:
+    assert get_workspace_path() == Path.home() / ".nanobot" / "workspace"
+    assert get_workspace_path("~/custom-workspace") == Path.home() / "custom-workspace"