diff --git a/config/security.toml b/config/security.toml
new file mode 100644
index 0000000..7eb8935
--- /dev/null
+++ b/config/security.toml
@@ -0,0 +1,107 @@
+# ZCLAW Security Configuration
+# Controls which commands and operations are allowed
+
+[shell_exec]
+# Enable shell command execution
+enabled = true
+# Default timeout in seconds
+default_timeout = 60
+# Maximum output size in bytes
+max_output_size = 1048576  # 1MB
+
+# Whitelist of allowed commands
+# If whitelist is non-empty, only these commands are allowed
+allowed_commands = [
+    "git",
+    "npm",
+    "pnpm",
+    "node",
+    "cargo",
+    "rustc",
+    "python",
+    "python3",
+    "pip",
+    "ls",
+    "cat",
+    "echo",
+    "mkdir",
+    "rm",
+    "cp",
+    "mv",
+    "grep",
+    "find",
+    "head",
+    "tail",
+    "wc",
+]
+
+# Blacklist of dangerous commands (always blocked)
+blocked_commands = [
+    "rm -rf /",
+    "dd",
+    "mkfs",
+    "format",
+    "shutdown",
+    "reboot",
+    "init",
+    "systemctl",
+]
+
+[file_read]
+enabled = true
+# Allowed directory prefixes (empty = allow all)
+allowed_paths = []
+# Blocked paths (always blocked)
+blocked_paths = [
+    "/etc/shadow",
+    "/etc/passwd",
+    "~/.ssh",
+    "~/.gnupg",
+]
+
+[file_write]
+enabled = true
+# Maximum file size in bytes (10MB)
+max_file_size = 10485760
+# Blocked paths
+blocked_paths = [
+    "/etc",
+    "/usr",
+    "/bin",
+    "/sbin",
+    "C:\\Windows",
+    "C:\\Program Files",
+]
+
+[web_fetch]
+enabled = true
+# Request timeout in seconds
+timeout = 30
+# Maximum response size in bytes (10MB)
+max_response_size = 10485760
+# Block internal/private IP ranges (SSRF protection)
+block_private_ips = true
+# Allowed domains (empty = allow all)
+allowed_domains = []
+# Blocked domains
+blocked_domains = []
+
+[browser]
+# Browser automation settings
+enabled = true
+# Default page load timeout in seconds
+page_timeout = 30
+# Maximum concurrent sessions
+max_sessions = 5
+# Block access to internal networks
+block_internal_networks = true
+
+[mcp]
+# MCP protocol settings
+enabled = true
+# Allowed MCP servers (empty = allow all)
+allowed_servers = []
+# Blocked MCP servers
+blocked_servers = []
+# Maximum tool execution time in seconds
+max_tool_time = 300
diff --git a/crates/zclaw-runtime/Cargo.toml b/crates/zclaw-runtime/Cargo.toml
index 7d37d54..70056c3 100644
--- a/crates/zclaw-runtime/Cargo.toml
+++ b/crates/zclaw-runtime/Cargo.toml
@@ -17,6 +17,7 @@ futures = { workspace = true }
 async-stream = { workspace = true }
 serde = { workspace = true }
 serde_json = { workspace = true }
+toml = { workspace = true }
 thiserror = { workspace = true }
 uuid = { workspace = true }
 chrono = { workspace = true }
diff --git a/crates/zclaw-runtime/src/tool/builtin/shell_exec.rs b/crates/zclaw-runtime/src/tool/builtin/shell_exec.rs
index 77bf1db..7802a0c 100644
--- a/crates/zclaw-runtime/src/tool/builtin/shell_exec.rs
+++ b/crates/zclaw-runtime/src/tool/builtin/shell_exec.rs
@@ -1,16 +1,129 @@
-//! Shell execution tool
+//! Shell execution tool with security controls
 
 use async_trait::async_trait;
+use serde::{Deserialize, Serialize};
 use serde_json::{json, Value};
+use std::collections::HashSet;
+use std::io::{Read, Write};
+use std::process::{Command, Stdio};
+use std::time::{Duration, Instant};
 use zclaw_types::{Result, ZclawError};
 
 use crate::tool::{Tool, ToolContext};
 
-pub struct ShellExecTool;
+/// Security configuration for shell execution
+#[derive(Debug, Clone, Deserialize)]
+pub struct ShellSecurityConfig {
+    pub enabled: bool,
+    pub default_timeout: u64,
+    pub max_output_size: usize,
+    pub allowed_commands: Vec<String>,
+    pub blocked_commands: Vec<String>,
+}
+
+impl Default for ShellSecurityConfig {
+    fn default() -> Self {
+        Self {
+            enabled: true,
+            default_timeout: 60,
+            max_output_size: 1024 * 1024, // 1MB
+            allowed_commands: vec![
+                "git".to_string(), "npm".to_string(), "pnpm".to_string(),
+                "node".to_string(), "cargo".to_string(), "rustc".to_string(),
+                "python".to_string(), "python3".to_string(), "pip".to_string(),
+                "ls".to_string(), "cat".to_string(), "echo".to_string(),
+                "mkdir".to_string(), "rm".to_string(), "cp".to_string(),
+                "mv".to_string(), "grep".to_string(), "find".to_string(),
+                "head".to_string(), "tail".to_string(), "wc".to_string(),
+            ],
+            blocked_commands: vec![
+                "rm -rf /".to_string(), "dd".to_string(), "mkfs".to_string(),
+                "shutdown".to_string(), "reboot".to_string(),
+                "format".to_string(), "init".to_string(),
+            ],
+        }
+    }
+}
+
+impl ShellSecurityConfig {
+    /// Load from config file
+    pub fn load() -> Self {
+        // Try to load from config/security.toml
+        if let Ok(content) = std::fs::read_to_string("config/security.toml") {
+            if let Ok(config) = toml::from_str::<SecurityConfigFile>(&content) {
+                return config.shell_exec;
+            }
+        }
+        Self::default()
+    }
+
+    /// Check if a command is allowed
+    pub fn is_command_allowed(&self, command: &str) -> Result<()> {
+        if !self.enabled {
+            return Err(ZclawError::SecurityError(
+                "Shell execution is disabled".to_string()
+            ));
+        }
+
+        // Parse the base command
+        let base_cmd = command.split_whitespace().next().unwrap_or("");
+
+        // Check blocked commands first
+        for blocked in &self.blocked_commands {
+            if command.starts_with(blocked) || command.contains(blocked) {
+                return Err(ZclawError::SecurityError(
+                    format!("Command blocked: {}", blocked)
+                ));
+            }
+        }
+
+        // If whitelist is non-empty, check against it
+        if !self.allowed_commands.is_empty() {
+            let allowed: HashSet<&str> = self.allowed_commands
+                .iter()
+                .map(|s| s.as_str())
+                .collect();
+
+            // Extract base command name (strip path if present)
+            let cmd_name = if base_cmd.contains('/') || base_cmd.contains('\\') {
+                base_cmd.rsplit(|c| c == '/' || c == '\\').next().unwrap_or(base_cmd)
+            } else if cfg!(windows) && base_cmd.ends_with(".exe") {
+                &base_cmd[..base_cmd.len() - 4]
+            } else {
+                base_cmd
+            };
+
+            if !allowed.contains(cmd_name) && !allowed.contains(base_cmd) {
+                return Err(ZclawError::SecurityError(
+                    format!("Command not in whitelist: {}", base_cmd)
+                ));
+            }
+        }
+
+        Ok(())
+    }
+}
+
+/// Security config file structure
+#[derive(Debug, Deserialize)]
+struct SecurityConfigFile {
+    shell_exec: ShellSecurityConfig,
+}
+
+pub struct ShellExecTool {
+    config: ShellSecurityConfig,
+}
 
 impl ShellExecTool {
     pub fn new() -> Self {
-        Self
+        Self {
+            config: ShellSecurityConfig::load(),
+        }
+    }
+
+    /// Create with custom config (for testing)
+    pub fn with_config(config: ShellSecurityConfig) -> Self {
+        Self { config }
     }
 }
 
@@ -21,7 +134,7 @@ impl Tool for ShellExecTool {
     }
 
     fn description(&self) -> &str {
-        "Execute a shell command and return the output"
+        "Execute a shell command with security controls and return the output"
     }
 
     fn input_schema(&self) -> Value {
@@ -34,7 +147,11 @@ impl Tool for ShellExecTool {
                 },
                 "timeout": {
                     "type": "integer",
-                    "description": "Timeout in seconds (default: 30)"
+                    "description": "Timeout in seconds (default: 60)"
+                },
+                "cwd": {
+                    "type": "string",
+                    "description": "Working directory for the command"
                 }
             },
             "required": ["command"]
@@ -45,11 +162,79 @@ impl Tool for ShellExecTool {
         let command = input["command"].as_str()
             .ok_or_else(|| ZclawError::InvalidInput("Missing 'command' parameter".into()))?;
 
-        // TODO: Implement actual shell execution with security constraints
+        let timeout_secs = input["timeout"].as_u64().unwrap_or(self.config.default_timeout);
+        let cwd = input["cwd"].as_str();
+
+        // Security check
+        self.config.is_command_allowed(command)?;
+
+        // Parse command into program and args
+        let parts: Vec<&str> = command.split_whitespace().collect();
+        if parts.is_empty() {
+            return Err(ZclawError::InvalidInput("Empty command".into()));
+        }
+
+        let program = parts[0];
+        let args = &parts[1..];
+
+        // Build command
+        let mut cmd = Command::new(program);
+        cmd.args(args);
+
+        if let Some(dir) = cwd {
+            cmd.current_dir(dir);
+        }
+
+        // Set up pipes
+        cmd.stdin(Stdio::piped())
+            .stdout(Stdio::piped())
+            .stderr(Stdio::piped());
+
+        let start = Instant::now();
+
+        // Execute command
+        let output = tokio::task::spawn_blocking(move || {
+            cmd.output()
+        })
+        .await
+        .map_err(|e| ZclawError::ToolError(format!("Task spawn error: {}", e)))?
+        .map_err(|e| ZclawError::ToolError(format!("Command execution failed: {}", e)))?;
+
+        let duration = start.elapsed();
+
+        // Check timeout
+        if duration > Duration::from_secs(timeout_secs) {
+            return Err(ZclawError::Timeout(
+                format!("Command timed out after {} seconds", timeout_secs)
+            ));
+        }
+
+        // Truncate output if too large
+        let stdout = String::from_utf8_lossy(&output.stdout);
+        let stderr = String::from_utf8_lossy(&output.stderr);
+
+        let stdout = if stdout.len() > self.config.max_output_size {
+            format!("{}...\n[Output truncated, exceeded {} bytes]",
+                &stdout[..self.config.max_output_size],
+                self.config.max_output_size)
+        } else {
+            stdout.to_string()
+        };
+
+        let stderr = if stderr.len() > self.config.max_output_size {
+            format!("{}...\n[Output truncated, exceeded {} bytes]",
+                &stderr[..self.config.max_output_size],
+                self.config.max_output_size)
+        } else {
+            stderr.to_string()
+        };
+
         Ok(json!({
-            "stdout": format!("Command output placeholder for: {}", command),
-            "stderr": "",
-            "exit_code": 0
+            "stdout": stdout,
+            "stderr": stderr,
+            "exit_code": output.status.code().unwrap_or(-1),
+            "duration_ms": duration.as_millis(),
+            "success": output.status.success()
         }))
     }
 }
@@ -59,3 +244,32 @@ impl Default for ShellExecTool {
         Self::new()
     }
 }
+
+#[cfg(test)]
+mod tests {
+    use super::*;
+
+    #[test]
+    fn test_security_config_default() {
+        let config = ShellSecurityConfig::default();
+        assert!(config.enabled);
+        assert!(!config.allowed_commands.is_empty());
+        assert!(!config.blocked_commands.is_empty());
+    }
+
+    #[test]
+    fn test_command_allowed() {
+        let config = ShellSecurityConfig::default();
+
+        // Should allow whitelisted commands
+        assert!(config.is_command_allowed("ls -la").is_ok());
+        assert!(config.is_command_allowed("git status").is_ok());
+
+        // Should block dangerous commands
+        assert!(config.is_command_allowed("rm -rf /").is_err());
+        assert!(config.is_command_allowed("shutdown").is_err());
+
+        // Should block non-whitelisted commands
+        assert!(config.is_command_allowed("dangerous_command").is_err());
+    }
+}
diff --git a/crates/zclaw-types/src/error.rs b/crates/zclaw-types/src/error.rs
index 84ae434..9a71bfc 100644
--- a/crates/zclaw-types/src/error.rs
+++ b/crates/zclaw-types/src/error.rs
@@ -52,6 +52,9 @@ pub enum ZclawError {
 
     #[error("MCP error: {0}")]
     McpError(String),
+
+    #[error("Security error: {0}")]
+    SecurityError(String),
 }
 
 /// Result type alias for ZCLAW operations