Microsoft Entra ID Setup Guide

Microsoft Entra ID Setup Guide

This guide provides step-by-step instructions for setting up Microsoft Entra ID (formerly Azure Active Directory) authentication for the MCP Gateway Registry.

Table of Contents

1. Prerequisites
2. Azure Portal Configuration
3. Environment Configuration
4. Group Configuration
5. Testing the Setup
6. Troubleshooting
7. Using the IAM API to Manage Groups, Users, and M2M Accounts
8. Generating JWT Tokens for M2M Accounts

Prerequisites

Before you begin, ensure you have:

• Access to an Azure account with permissions to create App Registrations
• Azure Active Directory (Entra ID) tenant
• Admin rights to configure App Registrations and assign users to groups
• The MCP Gateway Registry codebase

Azure Portal Configuration

Step 1: Create an App Registration

1. Navigate to the Azure Portal
2. Go to Azure Active Directory → App registrations
3. Click New registration
4. Configure the app registration:
   • Name: mcp-gateway-web (or your preferred name)
   • Supported account types: Select the appropriate option:
     • Single tenant (recommended): Only users in your organization
     • Multi-tenant: Users from any Azure AD tenant
   • Redirect URI:
     • Platform: Web
     • URI: http://localhost/auth/callback (for local development)
     • For production, use: https://your-domain.com/auth/callback
5. Click Register

Step 2: Note Your Application IDs

After creating the app registration, note the following values (you'll need them later):

1. From the app registration Overview page:
   • Application (client) ID: This is your ENTRA_CLIENT_ID
   • Directory (tenant) ID: This is your ENTRA_TENANT_ID

Step 3: Create a Client Secret

1. In your app registration, click Certificates & secrets in the left menu
2. Click New client secret
3. Configure the secret:
   • Description: mcp-gateway-auth (or your preferred description)
   • Expires: Choose an appropriate expiration period (recommended: 24 months)
4. Click Add
5. IMPORTANT: Copy the Value immediately (not the Secret ID)
   • This is your ENTRA_CLIENT_SECRET
   • You cannot retrieve this value later - if you lose it, you'll need to create a new secret

Step 4: Configure Redirect URIs

1. In your app registration, click Authentication in the left menu
2. Under Platform configurations → Web, add redirect URIs:
   • For local development: http://localhost/auth/callback
   • For production: https://your-domain.com/auth/callback
3. Under Implicit grant and hybrid flows, ensure nothing is checked (not needed for authorization code flow)
4. Click Save

Step 5: Add API Permissions

To get user email and group information, you need to configure API permissions:

1. Click API permissions in the left menu
2. Click Add a permission
3. Select Microsoft Graph
4. Select Delegated permissions
5. Search for and add the following permissions:
   • User.Read (should already be present)
   • email - Read user's email address
   • profile - Read user's basic profile
   • GroupMember.Read.All - Read groups user belongs to
6. Click Add permissions
7. CRITICAL: Click Grant admin consent for [Your Tenant]
   • This step is required for the permissions to work
   • You need admin privileges to grant consent

Step 6: Configure Optional Claims

To include email, username, and groups in the ID token:

1. Click Token configuration in the left menu
2. Click Add optional claim
3. Select ID token type
4. Add these claims:
   • email - User's email address
   • preferred_username - User's UPN (User Principal Name)
   • groups - Security group Object IDs
5. Click Add
6. When prompted "Turn on the Microsoft Graph email, profile permission", click Add

Step 7: Configure Group Claims

1. Still in Token configuration
2. Click Add groups claim
3. Select Security groups
4. Under "Customize token properties by type":
   • ID: Check "Group ID"
   • Access: Check "Group ID"
5. Click Add

Step 8: Create Security Groups

Create Azure AD security groups for authorization:

1. Go to Azure Active Directory → Groups
2. Click New group
3. Create an admin group:
   • Group type: Security
   • Group name: Mcp-test-admin (or your preferred name)
   • Group description: MCP Gateway administrators
   • Membership type: Assigned
4. Click Create
5. Repeat for a users group:
   • Group name: mcp-test-users (or your preferred name)
   • Group description: MCP Gateway users

Step 9: Note Group Object IDs

For each group you created:

1. Click on the group name
2. From the Overview page, copy the Object Id
3. Note these IDs - you'll need them for scopes.yml configuration

Step 10: Add Users to Groups

1. For each group, click on the group name
2. Click Members in the left menu
3. Click Add members
4. Search for and select users
5. Click Select

Step 11: Configure App for API Access (Optional)

If you plan to use machine-to-machine (M2M) authentication:

1. Click Expose an API in the left menu
2. Click Add next to "Application ID URI"
3. Accept the default (api://{client-id}) or customize it
4. Click Save
5. Click Add a scope
6. Configure the scope:
   • Scope name: .default
   • Who can consent: Admins only
   • Admin consent display name: Access MCP Gateway
   • Admin consent description: Allow the application to access MCP Gateway
   • State: Enabled
7. Click Add scope

Environment Configuration

Step 1: Update .env File

1. Copy .env.example to .env if you haven't already:

   cp .env.example .env
   

2. Edit the .env file and configure Entra ID settings:

# =============================================================================
# AUTHENTICATION PROVIDER CONFIGURATION
# =============================================================================
# Choose authentication provider: 'cognito', 'keycloak', or 'entra'
AUTH_PROVIDER=entra

# =============================================================================
# MICROSOFT ENTRA ID CONFIGURATION
# =============================================================================

# Azure AD Tenant ID (from Azure Portal → App registration → Overview)
ENTRA_TENANT_ID=12345678-1234-1234-1234-123456789012

# Entra ID Application (client) ID (from Azure Portal → App registration → Overview)
ENTRA_CLIENT_ID=87654321-4321-4321-4321-210987654321

# Entra ID Client Secret (from Azure Portal → App registration → Certificates & secrets)
ENTRA_CLIENT_SECRET=your-secret-value-here

# Enable Entra ID in OAuth2 providers
ENTRA_ENABLED=true

# Azure AD Group Object IDs (from Azure Portal → Groups → Overview)
# IMPORTANT: ENTRA_GROUP_ADMIN_ID is required for admin access to persist across restarts.
# This group ID is added to the registry-admins scope in MongoDB during initialization.
# Users in this Entra group will have full admin access to the MCP Gateway.
ENTRA_GROUP_ADMIN_ID=16c7e67e-e8ae-498c-ba2e-0593c0159e43
ENTRA_GROUP_USERS_ID=62c07ac1-03d0-4924-90c7-a0255f23bd1d

3. Update other required settings:

# =============================================================================
# REGISTRY CONFIGURATION
# =============================================================================
# For local development
REGISTRY_URL=http://localhost

# For production with custom domain
# REGISTRY_URL=https://mcpgateway.mycorp.com

# =============================================================================
# AUTH SERVER CONFIGURATION
# =============================================================================
# For local development
AUTH_SERVER_EXTERNAL_URL=http://localhost

# For production with custom domain
# AUTH_SERVER_EXTERNAL_URL=https://mcpgateway.mycorp.com

# =============================================================================
# APPLICATION SECURITY
# =============================================================================
# CRITICAL: CHANGE THIS SECRET KEY IMMEDIATELY!
SECRET_KEY=your-super-secure-random-64-character-string-here

Group Configuration

Configure scopes.yml

The auth_server/scopes.yml file maps Azure AD groups to MCP Gateway scopes and permissions.

1. Open auth_server/scopes.yml

2. Update the Entra ID group mappings section with your group Object IDs:

group_mappings:
  # Entra ID group mappings (by Azure AD Group Object IDs)
  # Admin group
  "object_id":
  - mcp-registry-admin
  - registry-admins

3. Replace the group Object IDs with your actual group IDs from Azure Portal

Understanding Scope Mappings

• mcp-registry-admin: Full administrative access to the registry

  • Can list, register, modify, and toggle services
  • Has unrestricted read and execute access to MCP servers

• mcp-registry-user: Limited user access

  • Can list and view specific services
  • Has restricted read access to MCP servers

• mcp-registry-developer: Development access

  • Can list, register, and health check services
  • Has restricted read and execute access

• mcp-registry-operator: Operations access

  • Can list, health check, and toggle services
  • Has restricted read and execute access

Testing the Setup

Step 1: Start the Services

1. Build and start the Docker containers:

   docker-compose up -d --build
   

2. Check that services are running:

   docker-compose ps
   

Step 2: Test User Authentication

1. Open your browser and navigate to:

   http://localhost
   

2. You should see the MCP Gateway Registry login page

3. Click the Sign in with Microsoft Entra ID button

4. You will be redirected to Microsoft's login page

5. Sign in with a user account that belongs to one of your configured groups

6. After successful authentication, you should be redirected back to the registry

Step 3: Verify User Information

1. Check the auth server logs to verify user information is being received:

   docker-compose logs auth-server | grep "Raw user info"
   

2. You should see output similar to:

   Raw user info from entra: {
     'sub': 'abc123...',
     'email': 'user@yourdomain.onmicrosoft.com',
     'preferred_username': 'user@yourdomain.onmicrosoft.com',
     'groups': ['16c7e67e-...', '62c07ac1-...'],
     'name': 'First Last'
   }
   

3. Verify the mapped scopes:

   docker-compose logs auth-server | grep "Mapped user info"
   

4. You should see:

   Mapped user info: {
     'username': 'user@yourdomain.onmicrosoft.com',
     'email': 'user@yourdomain.onmicrosoft.com',
     'name': 'First Last',
     'groups': ['mcp-registry-admin', 'mcp-servers-unrestricted/read', ...]
   }
   

Step 4: Test Authorization

1. Log in with an admin user (member of the admin group)

2. Verify you can access admin functions:

   • Register new services
   • Modify service configurations
   • Toggle services on/off

3. Log in with a regular user (member of the users group)

4. Verify restricted access:

   • Can view services
   • Cannot register or modify services

Step 5: Test Machine-to-Machine (M2M) Authentication

If you configured API access for M2M authentication:

1. Create a service principal for your AI agent:

   # This is done in Azure Portal → App registrations
   # Create a new app registration for the AI agent
   

2. Test M2M token generation:

   curl -X POST "https://login.microsoftonline.com/{tenant-id}/oauth2/v2.0/token" \
     -H "Content-Type: application/x-www-form-urlencoded" \
     -d "grant_type=client_credentials" \
     -d "client_id={agent-client-id}" \
     -d "client_secret={agent-client-secret}" \
     -d "scope=api://{mcp-gateway-client-id}/.default"
   

3. Use the access token to call MCP Gateway APIs

Troubleshooting

Issue: Missing email and groups claims

Symptoms:

Raw user info from entra: {'sub': '...', 'name': 'User Name', 'family_name': '...', 'given_name': '...'}
Mapped user info: {'username': None, 'email': None, 'groups': []}

Solution:

1. Verify you completed Step 5: Add API Permissions
2. Ensure you clicked Grant admin consent
3. Complete Step 6: Configure Optional Claims
4. Complete Step 7: Configure Group Claims
5. Wait 5-10 minutes for Azure AD to propagate changes
6. Clear browser cookies and try logging in again

Issue: Token validation fails with "Invalid issuer"

Symptoms:

Token validation failed: Invalid issuer: https://sts.windows.net/{tenant}/

Solution: The Entra ID provider supports both v1.0 and v2.0 token formats. This error should not occur with the current implementation. If you see this:

1. Check that ENTRA_TENANT_ID in .env matches your actual tenant ID
2. Verify the token is being issued by Microsoft Entra ID
3. Check auth server logs for more details

Issue: User cannot access any resources

Symptoms: User can log in but sees "Access Denied" or "Insufficient Permissions"

Solution:

1. Verify the user is added to at least one security group in Azure AD
2. Check that group Object IDs in scopes.yml match the groups in Azure Portal
3. Verify the group mappings include the necessary scopes
4. Check auth server logs to see what groups are being received:

   docker-compose logs auth-server | grep "groups"
   

Issue: Redirect URI mismatch error

Symptoms:

AADSTS50011: The redirect URI 'http://localhost/auth/callback' does not match the redirect URIs configured for the application

Solution:

1. Go to Azure Portal → App registrations → Your app → Authentication
2. Verify the redirect URI exactly matches what's in the error message
3. Add any missing redirect URIs
4. Ensure AUTH_SERVER_EXTERNAL_URL in .env matches the base URL

Issue: "Groups overage" claim

Symptoms: Groups claim contains _claim_names and _claim_sources instead of group IDs

Solution: This occurs when a user is a member of more than 200 groups. You need to:

1. Modify the auth provider to fetch groups via Microsoft Graph API
2. See the alternative implementation in docs/ENTRA-ID-APP-CONFIGURATION.md Step 5

Issue: Client secret expired

Symptoms:

AADSTS7000215: Invalid client secret provided

Solution:

1. Go to Azure Portal → App registrations → Your app → Certificates & secrets
2. Create a new client secret
3. Update ENTRA_CLIENT_SECRET in .env
4. Restart the services:

   docker-compose restart auth-server
   

Issue: Cannot grant admin consent

Symptoms: You don't see the "Grant admin consent" button or get an error when clicking it

Solution:

1. You need Global Administrator, Application Administrator, or Cloud Application Administrator role
2. Contact your Azure AD administrator to grant the permissions
3. Alternatively, users can consent individually (not recommended for production)

Additional Resources

• Microsoft Entra ID Documentation
• OAuth 2.0 Authorization Code Flow
• Optional Claims Configuration
• Configure Group Claims
• Microsoft Graph Permissions Reference

Production Deployment

Update Redirect URIs

For production, update redirect URIs:

https://your-domain.com/oauth2/callback/entra

Environment Variables

Update production .env:

ENTRA_REDIRECT_URI=https://your-domain.com/oauth2/callback/entra
AUTH_SERVER_EXTERNAL_URL=https://your-domain.com:8888

SSL/TLS Configuration

Ensure your production deployment uses HTTPS for all OAuth flows.

Advanced Configuration

Custom Claims

To add custom claims to tokens:

1. Go to Token configuration
2. Click Add optional claim
3. Select token type and claims
4. Configure claim conditions

Group Filtering

To limit which groups are included in tokens:

1. Go to Token configuration
2. Click Add groups claim
3. Configure Groups assigned to the application

Enterprise Applications

For advanced management:

1. Go to Enterprise applications
2. Find your app registration
3. Configure:
   • User assignment required
   • Visibility settings
   • Provisioning (if needed)

Adding New Users

Option 1: Add User to Existing Group (Recommended)

In Azure Portal:

1. Go to Microsoft Entra ID → Groups
2. Click on MCP Registry Admins (or appropriate group)
3. Click Members → Add members
4. Search and select the new user
5. Click Select

Access will be immediate - user can login and see servers/agents.

Option 2: Create New Group for User

If you need different permissions:

1. Create new group in Azure:

   • Group name: MCP Registry LOB3 Users
   • Members: Add the new user

2. Get the group Object ID from the group overview page

3. Add to scopes.yml:

group_mappings:
  # Add new group mapping
  "new-group-object-id-here":
  - registry-users-lob1  # or whatever permission level needed

4. Restart auth server:

cp auth_server/scopes.yml ~/mcp-gateway/auth_server/scopes.yml
docker-compose restart auth-server

API Reference

Token Endpoint

POST https://login.microsoftonline.com/{tenant-id}/oauth2/v2.0/token

Authorization Endpoint

GET https://login.microsoftonline.com/{tenant-id}/oauth2/v2.0/authorize

User Info Endpoint

GET https://graph.microsoft.com/v1.0/me

Security Best Practices

1. Client Secret Management

   • Store client secrets securely (use Azure Key Vault in production)
   • Rotate secrets regularly (set expiration and create new secrets)
   • Never commit secrets to version control

2. Token Configuration

   • Keep token expiration times reasonable (default: 1 hour for access tokens)
   • Use refresh tokens for long-running sessions
   • Implement proper token revocation

3. Group Management

   • Use security groups (not distribution lists or Microsoft 365 groups)
   • Apply principle of least privilege
   • Regularly audit group memberships

4. HTTPS in Production

   • Always use HTTPS in production environments
   • Configure proper SSL/TLS certificates
   • Update redirect URIs to use HTTPS

5. Monitoring and Logging

   • Enable Azure AD audit logs
   • Monitor sign-in logs for suspicious activity
   • Set up alerts for authentication failures

6. Multi-Factor Authentication

   • Enable MFA for all users (configured in Azure AD)
   • Use conditional access policies
   • Enforce MFA for admin accounts

Using the IAM API to Manage Groups, Users, and M2M Accounts

The MCP Gateway Registry provides an IAM API for managing groups, human users, and M2M (machine-to-machine) service accounts programmatically. This section covers how to use the registry_management.py CLI to perform these operations.

Prerequisites

Before using the IAM API commands, you need:

1. An admin access token: Either a self-signed token from the UI sidebar or a Keycloak/Entra ID token for an admin user
2. Registry URL: The URL of your MCP Gateway Registry deployment
3. Admin group membership: Your user must be in the registry-admins group

Save your token to a file for CLI usage:

# Save token from UI sidebar to a file
echo "eyJhbGci..." > api/.token

Creating a Group (Scope)

Groups define access permissions for users and M2M accounts. Create a group definition JSON file:

Example: cli/examples/public-mcp-users.json

{
  "scope_name": "public-mcp-users",
  "description": "Users with access to public MCP servers",
  "server_access": [
    {
      "server": "context7",
      "methods": ["initialize", "tools/list", "tools/call"],
      "tools": ["*"]
    },
    {
      "server": "api",
      "methods": ["initialize", "GET", "POST", "servers", "agents"],
      "tools": []
    },
    {
      "agents": {
        "actions": [
          {"action": "list_agents", "resources": ["/flight-booking"]},
          {"action": "get_agent", "resources": ["/flight-booking"]}
        ]
      }
    }
  ],
  "group_mappings": ["public-mcp-users"],
  "ui_permissions": {
    "list_service": ["all"],
    "list_agents": ["/flight-booking"],
    "get_agent": ["/flight-booking"]
  },
  "create_in_idp": true
}

Import the group:

uv run python api/registry_management.py \
  --token-file api/.token \
  --registry-url https://your-registry-url.example.com \
  import-group --file cli/examples/public-mcp-users.json

Key fields in group definition:

Creating a Human User

Human users can log in via the web UI using Entra ID authentication.

uv run python api/registry_management.py \
  --token-file api/.token \
  --registry-url https://your-registry-url.example.com \
  user-create-human \
  --username jsmith \
  --email jsmith@example.com \
  --first-name John \
  --last-name Smith \
  --groups public-mcp-users \
  --password "SecurePassword123!"

Parameters:

Creating an M2M Service Account

M2M (machine-to-machine) accounts are used for programmatic API access, AI coding assistants, and agent identities.

uv run python api/registry_management.py \
  --token-file api/.token \
  --registry-url https://your-registry-url.example.com \
  user-create-m2m \
  --name my-ai-agent \
  --groups public-mcp-users \
  --description "AI coding assistant service account"

Output:

Client ID: xxxxxxxx-xxxx-xxxx-xxxx-xxxxxxxxxxxx
Client Secret: xxxxx~xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx
Groups: public-mcp-users
Service Principal ID: xxxxxxxx-xxxx-xxxx-xxxx-xxxxxxxxxxxx

IMPORTANT: Save the client secret securely - it cannot be retrieved later.

Parameters:

Where to Find Parameter Values

Generating JWT Tokens for M2M Accounts

M2M accounts use OAuth2 client credentials flow to obtain JWT tokens. These tokens can be used for:

• Agent identities in A2A (Agent-to-Agent) communication
• AI coding assistants (Cursor, VS Code, etc.)
• Programmatic API access
• Automated scripts and CI/CD pipelines

Method 1: Direct Token Request (curl)

Request a token directly from Microsoft Entra ID:

curl -X POST "https://login.microsoftonline.com/{TENANT_ID}/oauth2/v2.0/token" \
  -H "Content-Type: application/x-www-form-urlencoded" \
  -d "client_id={M2M_CLIENT_ID}" \
  -d "client_secret={M2M_CLIENT_SECRET}" \
  -d "scope=api://{APP_CLIENT_ID}/.default" \
  -d "grant_type=client_credentials"

Example with placeholder values:

curl -X POST "https://login.microsoftonline.com/your-tenant-id/oauth2/v2.0/token" \
  -H "Content-Type: application/x-www-form-urlencoded" \
  -d "client_id=your-m2m-client-id" \
  -d "client_secret=your-m2m-client-secret" \
  -d "scope=api://your-app-client-id/.default" \
  -d "grant_type=client_credentials"

Response:

{
  "token_type": "Bearer",
  "expires_in": 3599,
  "access_token": "eyJ0eXAiOiJKV1QiLCJhbGciOi..."
}

Method 2: Using the Credentials Provider Script

The generate_creds.sh script automates token generation for multiple identities.

Step 1: Configure identities file

Create or edit .oauth-tokens/entra-identities.json:

[
  {
    "identity_name": "my-ai-agent",
    "tenant_id": "your-tenant-id",
    "client_id": "your-m2m-client-id",
    "client_secret": "your-m2m-client-secret",
    "scope": "api://your-app-client-id/.default"
  }
]

Identities File Structure:

Multiple Identities Example:

[
  {
    "identity_name": "cursor-assistant",
    "tenant_id": "your-tenant-id",
    "client_id": "cursor-m2m-client-id",
    "client_secret": "cursor-m2m-client-secret",
    "scope": "api://your-app-client-id/.default"
  },
  {
    "identity_name": "ci-pipeline",
    "tenant_id": "your-tenant-id",
    "client_id": "cicd-m2m-client-id",
    "client_secret": "cicd-m2m-client-secret",
    "scope": "api://your-app-client-id/.default"
  }
]

Step 2: Set auth provider

Ensure AUTH_PROVIDER=entra is set in your .env file.

Step 3: Run the script

./credentials-provider/generate_creds.sh

Or with a custom identities file:

uv run credentials-provider/entra/generate_tokens.py \
  --identities-file /path/to/my-identities.json \
  --output-dir .oauth-tokens \
  --verbose

Output:

• Tokens are saved to .oauth-tokens/{identity_name}.json
• Each file contains the access token, expiration time, and metadata

Token Scope Format

The scope for Entra ID M2M tokens follows this format:

api://{APP_CLIENT_ID}/.default

Where:

• {APP_CLIENT_ID} is the Application (client) ID of your MCP Gateway app registration
• .default requests all scopes that admin consent has been granted for

Using Tokens in AI Coding Assistants

Once you have a JWT token, you can use it in AI coding assistants like Cursor or VS Code extensions:

1. Configure the MCP server connection with the registry URL
2. Set the Bearer token in the authorization header
3. The token grants access based on the M2M account's group membership

Example configuration for an AI assistant:

{
  "mcp_registry_url": "https://your-registry-url.example.com",
  "auth_token": "eyJ0eXAiOiJKV1QiLCJhbGciOi..."
}

User-Generated Tokens from the UI

Users can also generate personal JWT tokens from the MCP Gateway Registry web UI:

1. Log in to the registry at https://your-registry-url.example.com
2. Navigate to the sidebar
3. Click on "Generate Token" or similar option
4. Copy the generated token

These self-signed tokens:

• Are signed with HS256 using the server's secret key
• Include the user's groups and scopes
• Can be used for programmatic API access
• Work with the same endpoints as M2M tokens

Next Steps

After completing the setup:

1. Configure Additional Services: Add more MCP servers to the registry
2. Set Up Custom Domain: Configure HTTPS and custom domain names
3. Configure M2M Authentication: Set up service principals for AI agents
4. Implement Monitoring: Set up observability and alerting
5. Production Deployment: Deploy to your production environment

For more information, see:

• Complete Setup Guide
• Observability Documentation
• FAQ