diff --git a/README.md b/README.md
index 7387f48..65abf4c 100644
--- a/README.md
+++ b/README.md
@@ -202,6 +202,7 @@ tools:
         my-server:
           command: npx
           args: ["-y", "my-mcp-server"]
+          cwd: /path/to/working/directory  # Optional working directory
 ```
 
 **Configuration options**:
@@ -213,6 +214,15 @@ tools:
 | `max_content_size` | `50000` | Maximum content size in characters. Content exceeding this limit is automatically truncated with a notice to prevent context window exhaustion |
 | `servers` | (optional) | Inline server configuration (overrides .amplifier/mcp.json) |
 
+**Per-server configuration options**:
+
+| Option | Required | Description |
+|--------|----------|-------------|
+| `command` | Yes | Command to execute (e.g., `npx`, `python`, `node`) |
+| `args` | No | Arguments for the command |
+| `env` | No | Environment variables for the server process |
+| `cwd` | No | Working directory for the server process. Falls back to `AMPLIFIER_WORK_DIRECTORY` env var if not specified |
+
 **Environment variable override**:
 ```bash
 # Enable verbose output without changing bundle config
diff --git a/amplifier_module_tool_mcp/client.py b/amplifier_module_tool_mcp/client.py
index 6e75d34..c25c0d5 100644
--- a/amplifier_module_tool_mcp/client.py
+++ b/amplifier_module_tool_mcp/client.py
@@ -49,6 +49,7 @@ def __init__(
         command: str,
         args: list[str],
         env: dict[str, str] | None = None,
+        cwd: str | Path | None = None,
         reconnection_config: ReconnectionConfig | None = None,
         verbose_servers: bool = False,
         server_log_dir: Path | None = None,
@@ -61,6 +62,7 @@ def __init__(
             command: Command to execute (e.g., "npx", "python")
             args: Arguments for the command
             env: Optional environment variables
+            cwd: Optional working directory for the server process
             reconnection_config: Reconnection configuration (uses defaults if None)
             verbose_servers: Whether to show server stderr output (default: False)
             server_log_dir: Directory for server logs when suppressed (default: ~/.amplifier/logs/mcp-servers/)
@@ -69,6 +71,7 @@ def __init__(
         self.command = command
         self.args = args
         self.env = env or {}
+        self.cwd = cwd
         self.session: ClientSession | None = None
         self.tools: list[dict[str, Any]] = []
         self.resources: list[dict[str, Any]] = []
@@ -143,6 +146,7 @@ async def _connection_task_impl(self) -> None:
                 command=self.command,
                 args=self.args,
                 env=merged_env,
+                cwd=self.cwd,
             )
 
             # Open log file if needed
diff --git a/amplifier_module_tool_mcp/manager.py b/amplifier_module_tool_mcp/manager.py
index baceda5..a7d89e3 100644
--- a/amplifier_module_tool_mcp/manager.py
+++ b/amplifier_module_tool_mcp/manager.py
@@ -152,9 +152,16 @@ async def _start_stdio_server(self, server_name: str, server_config: dict[str, A
         # Substitute environment variables
         env = {k: MCPConfig.substitute_env_vars(v) for k, v in env.items()}
 
+        # Get working directory from config, or fall back to AMPLIFIER_WORK_DIRECTORY env var
+        cwd = server_config.get("cwd")
+        if not cwd:
+            cwd = os.environ.get("AMPLIFIER_WORK_DIRECTORY")
+        if cwd:
+            logger.debug(f"Server '{server_name}' will use working directory: {cwd}")
+
         # Create and connect client with verbose settings
         client = MCPClient(
-            server_name, command, args, env, verbose_servers=self.verbose_servers, server_log_dir=self.server_log_dir
+            server_name, command, args, env, cwd=cwd, verbose_servers=self.verbose_servers, server_log_dir=self.server_log_dir
         )
         await client.connect()