diff --git a/DOCKER.md b/DOCKER.md
index edc1d9c..f4feac7 100644
--- a/DOCKER.md
+++ b/DOCKER.md
@@ -216,22 +216,82 @@ FROM python:3.11-slim
 
 ## Integration with Claude Desktop
 
-When running in Docker, configure Claude Desktop to connect to the containerized servers:
+Since MCP uses stdio for communication, connecting Claude Desktop to Docker containers requires special configuration.
+
+### Method 1: Docker Exec (Recommended)
+
+This method executes the Python script in an already-running container:
 
 ```json
 {
   "mcpServers": {
     "portainer-core": {
-      "url": "http://localhost:3000"
+      "command": "docker",
+      "args": ["exec", "-i", "portainer-mcp-core", "python", "portainer_core_server.py"]
+    },
+    "portainer-environments": {
+      "command": "docker",
+      "args": ["exec", "-i", "portainer-mcp-environments", "python", "portainer_environments_server.py"]
     },
     "portainer-docker": {
-      "url": "http://localhost:3002"
+      "command": "docker",
+      "args": ["exec", "-i", "portainer-mcp-docker", "python", "portainer_docker_server.py"]
+    },
+    "portainer-kubernetes": {
+      "command": "docker",
+      "args": ["exec", "-i", "portainer-mcp-kubernetes", "python", "portainer_kubernetes_server.py"]
+    },
+    "portainer-stacks": {
+      "command": "docker",
+      "args": ["exec", "-i", "portainer-mcp-stacks", "python", "portainer_stacks_server.py"]
+    },
+    "portainer-edge": {
+      "command": "docker",
+      "args": ["exec", "-i", "portainer-mcp-edge", "python", "portainer_edge_server.py"]
+    },
+    "portainer-gitops": {
+      "command": "docker",
+      "args": ["exec", "-i", "portainer-mcp-gitops", "python", "portainer_gitops_server.py"]
     }
-    // ... other servers
   }
 }
 ```
 
+**Prerequisites:**
+1. Containers must be running: `docker-compose up -d`
+2. Docker must be accessible from where Claude Desktop runs
+
+### Method 2: Docker Run (Alternative)
+
+This method creates a new container for each MCP session:
+
+```json
+{
+  "mcpServers": {
+    "portainer-core": {
+      "command": "docker",
+      "args": [
+        "run", "--rm", "-i",
+        "--env-file", "/path/to/portainer-mcp/.env",
+        "--network", "portainer-mcp_portainer-mcp",
+        "git.oe74.net/adelorenzo/portainer-mcp/portainer-core:latest"
+      ]
+    }
+    // ... similar for other servers
+  }
+}
+```
+
+**Pros:** Doesn't require pre-running containers
+**Cons:** Slower startup, creates new container each time
+
+### Important Notes
+
+- The `-i` flag is **required** for stdio communication
+- Ensure Docker daemon is running and accessible
+- For Windows/Mac users, Docker Desktop must be running
+- Container names must match those in docker-compose.yml
+
 ## Monitoring
 
 Monitor container health and resource usage:
diff --git a/README.md b/README.md
index 924cc7d..f6625e4 100644
--- a/README.md
+++ b/README.md
@@ -161,6 +161,8 @@ MAX_RETRIES=3
 
 ### Claude Desktop Configuration
 
+#### Option 1: Local Python Installation
+
 Add the servers to your Claude Desktop configuration (`claude_desktop_config.json`):
 
 ```json
@@ -181,27 +183,62 @@ Add the servers to your Claude Desktop configuration (`claude_desktop_config.jso
         "PORTAINER_URL": "https://your-portainer-instance.com",
         "PORTAINER_API_KEY": "your-api-key"
       }
-    },
-    "portainer-kubernetes": {
-      "command": "/path/to/.venv/bin/python",
-      "args": ["/path/to/portainer_kubernetes_server.py"],
-      "env": {
-        "PORTAINER_URL": "https://your-portainer-instance.com",
-        "PORTAINER_API_KEY": "your-api-key"
-      }
-    },
-    "portainer-gitops": {
-      "command": "/path/to/.venv/bin/python",
-      "args": ["/path/to/portainer_gitops_server.py"],
-      "env": {
-        "PORTAINER_URL": "https://your-portainer-instance.com",
-        "PORTAINER_API_KEY": "your-api-key"
-      }
     }
+    // Add other servers as needed...
   }
 }
 ```
 
+#### Option 2: Docker Containers (Recommended)
+
+**Note:** MCP protocol uses stdio for communication, which requires special handling for Docker containers. 
+
+For Docker deployment, you have two approaches:
+
+**Approach A: Docker Exec Method**
+```json
+{
+  "mcpServers": {
+    "portainer-core": {
+      "command": "docker",
+      "args": ["exec", "-i", "portainer-mcp-core", "python", "portainer_core_server.py"],
+      "env": {}
+    },
+    "portainer-docker": {
+      "command": "docker",
+      "args": ["exec", "-i", "portainer-mcp-docker", "python", "portainer_docker_server.py"],
+      "env": {}
+    }
+    // Add other servers as needed...
+  }
+}
+```
+
+**Approach B: Docker Run Method (creates new container each time)**
+```json
+{
+  "mcpServers": {
+    "portainer-core": {
+      "command": "docker",
+      "args": [
+        "run", "--rm", "-i",
+        "--env-file", "/path/to/portainer-mcp/.env",
+        "--network", "portainer-mcp_portainer-mcp",
+        "git.oe74.net/adelorenzo/portainer-mcp/portainer-core:latest"
+      ],
+      "env": {}
+    }
+    // Add other servers as needed...
+  }
+}
+```
+
+**Important Notes for Docker:**
+- Ensure containers are running: `docker-compose up -d`
+- The `-i` flag is crucial for interactive stdio communication
+- Approach A is faster but requires containers to be already running
+- Approach B is slower but doesn't require pre-running containers
+
 ## Usage Examples
 
 ### User Management (Core Server)