diff --git a/REFERENCE.md b/REFERENCE.md
index d0db46b..1e390e1 100644
--- a/REFERENCE.md
+++ b/REFERENCE.md
@@ -166,15 +166,15 @@ DSGo supports MCP clients for accessing external tools and services:
 | Exa | `NewMCPExaClient(apiKey)` | HTTP | Web search and content extraction |
 | Jina | `NewMCPJinaClient(apiKey)` | SSE | URL reading and content extraction |
 | Tavily | `NewMCPTavilyClient(apiKey)` | HTTP | Web search and content extraction |
-| Filesystem | `NewMCPFilesystemClient(dirs...)` | Stdio | Local filesystem operations via official MCP server |
+| Filesystem | `NewMCPFilesystemClient(dir)` | Stdio | Local filesystem operations via official MCP server |
 
 ### Filesystem MCP Client
 
 Uses the official `@modelcontextprotocol/server-filesystem` via npx/bunx:
 
 ```go
-// Create filesystem client with allowed directories
-fsClient, err := dsgo.NewMCPFilesystemClient("/path/to/dir1", "/path/to/dir2")
+// Create filesystem client with specific directory
+fsClient, err := dsgo.NewMCPFilesystemClient("/path/to/directory")
 
 // Or use current directory (default)
 fsClient, err := dsgo.NewMCPFilesystemClient()
diff --git a/dsgo.go b/dsgo.go
index 3b8d839..cfa8985 100644
--- a/dsgo.go
+++ b/dsgo.go
@@ -273,7 +273,7 @@ var (
 	// Provides tavily-search and tavily-extract tools.
 	NewMCPTavilyClient = mcp.NewTavilyClient
 	// NewMCPFilesystemClient creates a new MCP client for local filesystem operations.
-	// Uses the official @modelcontextprotocol/server-filesystem via npx/bunx.
+	// The directory parameter specifies both allowed directory and working directory.
 	NewMCPFilesystemClient = mcp.NewFilesystemClient
 	// NewMCPHTTPTransport creates a new HTTP transport for MCP communication.
 	NewMCPHTTPTransport = mcp.NewHTTPTransport
@@ -285,6 +285,8 @@ var (
 	NewMCPSSETransportWithTimeouts = mcp.NewSSETransportWithTimeouts
 	// NewMCPStdioTransport creates a new stdio transport for MCP communication.
 	NewMCPStdioTransport = mcp.NewStdioTransport
+	// NewMCPStdioTransportWithDir creates a new stdio transport with a specific working directory.
+	NewMCPStdioTransportWithDir = mcp.NewStdioTransportWithDir
 	// NewMCPLocalTransport creates a local MCP transport.
 	NewMCPLocalTransport = mcp.NewLocalTransport
 	// NewMCPShellServer creates a built-in shell MCP server.
diff --git a/examples/yaml_program/tools.go b/examples/yaml_program/tools.go
index 75cd4cd..6e5dcbb 100644
--- a/examples/yaml_program/tools.go
+++ b/examples/yaml_program/tools.go
@@ -112,11 +112,11 @@ func createMCPClient(ctx context.Context, name string, spec MCPSpec, timeouts Ti
 		if err != nil {
 			return nil, fmt.Errorf("failed to find project root: %w", err)
 		}
-		allowedDirs := []string{projectRoot}
+		allowedDir := projectRoot
 		if len(spec.AllowedDirs) > 0 {
-			allowedDirs = spec.AllowedDirs
+			allowedDir = spec.AllowedDirs[0] // Use first directory as primary
 		}
-		client, err := dsgo.NewMCPFilesystemClient(allowedDirs...)
+		client, err := dsgo.NewMCPFilesystemClient(allowedDir)
 		if err != nil {
 			return nil, fmt.Errorf("failed to create filesystem MCP client: %w", err)
 		}
diff --git a/internal/mcp/client.go b/internal/mcp/client.go
index 126e6f6..fff79f1 100644
--- a/internal/mcp/client.go
+++ b/internal/mcp/client.go
@@ -68,16 +68,17 @@ func NewTavilyClient(apiKey string) (*Client, error) {
 
 // NewFilesystemClient creates a new MCP client for local filesystem operations.
 // Uses the official @modelcontextprotocol/server-filesystem via npx/bunx with stdio transport.
-// allowedDirs specifies the directories that the filesystem server can access.
-// If no directories are provided, defaults to current working directory.
-func NewFilesystemClient(allowedDirs ...string) (*Client, error) {
+// The directory parameter specifies both the allowed directory and the working directory
+// for the MCP server, so relative paths resolve correctly within it.
+// If empty, defaults to current working directory.
+func NewFilesystemClient(directory string) (*Client, error) {
 	// Default to current directory if none specified
-	if len(allowedDirs) == 0 {
+	if directory == "" {
 		cwd, err := os.Getwd()
 		if err != nil {
 			return nil, fmt.Errorf("failed to get current directory: %w", err)
 		}
-		allowedDirs = []string{cwd}
+		directory = cwd
 	}
 
 	// Try bunx first (Bun's npx equivalent), fall back to npx
@@ -89,12 +90,12 @@ func NewFilesystemClient(allowedDirs ...string) (*Client, error) {
 		}
 	}
 
-	// Build args: npx -y @modelcontextprotocol/server-filesystem <dir1> <dir2> ...
-	args := []string{"-y", "@modelcontextprotocol/server-filesystem"}
-	args = append(args, allowedDirs...)
+	// Build args: npx -y @modelcontextprotocol/server-filesystem <directory>
+	args := []string{"-y", "@modelcontextprotocol/server-filesystem", directory}
 
-	// Create stdio transport
-	transport, err := NewStdioTransport(command, args, os.Environ())
+	// Create stdio transport with working directory set to the allowed directory.
+	// This ensures relative paths are resolved correctly from the directory root.
+	transport, err := NewStdioTransportWithDir(command, args, os.Environ(), directory)
 	if err != nil {
 		return nil, fmt.Errorf("failed to create stdio transport: %w", err)
 	}
diff --git a/internal/mcp/transport.go b/internal/mcp/transport.go
index 093386b..db219bd 100644
--- a/internal/mcp/transport.go
+++ b/internal/mcp/transport.go
@@ -530,8 +530,17 @@ type StdioTransport struct {
 
 // NewStdioTransport creates a new StdioTransport.
 func NewStdioTransport(command string, args []string, env []string) (*StdioTransport, error) {
+	return NewStdioTransportWithDir(command, args, env, "")
+}
+
+// NewStdioTransportWithDir creates a new StdioTransport with a specific working directory.
+// If dir is empty, the current working directory is used.
+func NewStdioTransportWithDir(command string, args []string, env []string, dir string) (*StdioTransport, error) {
 	cmd := exec.Command(command, args...)
 	cmd.Env = env
+	if dir != "" {
+		cmd.Dir = dir
+	}
 
 	stdin, err := cmd.StdinPipe()
 	if err != nil {