How to Implement Conditional Access for Intune App Protection Policies (2025 Guide)

In-Depth Guide: Implementing Conditional Access Policies for App Protection Policies

Conditional Access (CA) and Intune App Protection Policies (APP) work together to create layered security for corporate data. CA acts as the gatekeeper, controlling who can access cloud resources, while APP enforces data protection controls within apps after access is granted. This guide covers planning, policy design, deployment, and monitoring for comprehensive app-based security.

1. Understanding the Integration

1.1 Conditional Access Overview

Conditional Access evaluates identity signals in real-time:

• User identity: Who is requesting access
• Device status: Managed, compliant, or unmanaged
• Location: Trusted networks vs. unknown locations
• App type: Native mobile apps vs. web browsers
• Risk signals: Sign-in anomalies, leaked credentials

1.2 App Protection Policy Overview

App Protection Policies control data handling within apps:

• Data loss prevention: Block copy/paste, save, print
• Access requirements: PIN, biometric, encryption
• Conditional launch: Wipe data if device is jailbroken
• Offline grace periods: Time limits for app usage without connectivity

1.3 How They Work Together

CA determines IF access is granted; APP controls HOW data is handled once inside the app. This dual-layer approach protects corporate data on both managed and unmanaged devices.

2. Policy Architecture and Flow

2.1 Decision Flow

1. User attempts to access a cloud app (Exchange Online, SharePoint)
2. Conditional Access evaluates the request against policy conditions
3. If conditions are met, access is granted with specified controls
4. App Protection Policy enforces data handling rules within the app
5. Ongoing monitoring ensures continuous compliance

2.2 Key Policy Components

• Assignments: Which users, groups, and apps the policy covers
• Conditions: Device platforms, locations, client app types
• Access Controls: Grant access with specific requirements
• Session Controls: Ongoing monitoring and restrictions

3. Planning Your Implementation

3.1 Assess Your Environment

• Inventory supported apps: Identify which apps support Intune SDK or MAM
• Define user scenarios: Corporate devices, BYOD, contractor access
• Map data sensitivity: Classify apps by data protection requirements
• Review existing policies: Audit current CA and device compliance policies

3.2 Design Policy Strategy

• Layered approach: Start with high-risk apps and sensitive data
• Pilot groups: Test with IT staff before broad deployment
• Fallback plans: Ensure users have alternative access methods
• Compliance alignment: Match policies to regulatory requirements

4. Creating Conditional Access Policies for App Protection

4.1 Step-by-Step Configuration

1. Access Microsoft Entra Admin Center
   1. Navigate to Protection → Conditional Access
2. Create New Policy
   1. Click + New Policy
   1. Enter descriptive name: “Require APP for Mobile Office Apps”
3. Configure Assignments
   1. Users: Select target groups (pilot users, all users, exclude break-glass accounts)
   1. Cloud apps: Choose specific apps (Exchange Online, SharePoint, Teams)
4. Define Conditions
   1. Device platforms: iOS, Android (mobile scenarios)
   1. Client apps: Mobile apps and desktop clients, modern authentication clients
   1. Locations: All locations or exclude trusted networks
5. Set Access Controls
   1. Grant access: Select “Require approved client app” AND “Require app protection policy”
   1. Session: Configure app enforced restrictions if needed
6. Enable and Test
   1. Set to Report-only mode first for testing
   1. Monitor sign-in logs for impact assessment
   1. Switch to On after validation

4.2 Advanced Configuration Options

• Risk-based conditions: Include sign-in risk or user risk levels
• Device state: Require device compliance for corporate devices
• Multi-factor authentication: Add MFA requirements for sensitive apps
• Terms of use: Require acceptance of usage policies

5. Supported Scenarios and Apps

5.1 Common Use Cases

Scenario	Conditional Access	App Protection
BYOD iPhone accessing Exchange	Require approved client app + APP	PIN, encryption, block save to personal cloud
Corporate Android device	Device compliance + APP	Standard data protection, allow printing
Contractor tablet access	MFA + approved client app + APP	Restrict copy/paste, time-based access
Legacy client blocking	Block non-modern auth clients	N/A – access denied

5.2 Supported Client Apps

• Microsoft apps: Outlook, Teams, OneDrive, Word, Excel, PowerPoint
• Partner apps: Salesforce, Adobe, ServiceNow (with Intune SDK)
• Custom LOB apps: Wrapped with Intune App Wrapping Tool or built with Intune SDK

6. Monitoring and Troubleshooting

6.1 Monitoring Tools

• Sign-in logs: Track policy application and failures in Microsoft Entra
• App protection reports: Monitor APP policy compliance in Intune
• Conditional Access insights: View policy impact and user experience
• What If tool: Test policy behavior before deployment

6.2 Common Issues and Solutions

Problem: Users can’t access apps after policy deployment

• Solution: Verify app supports APP, check policy assignments, review exclusions

Problem: Corporate data appears in personal apps

• Solution: Strengthen APP controls (block copy/paste), verify app wrapping

Problem: Frequent authentication prompts

• Solution: Adjust token lifetime, configure persistent browser sessions

Problem: Legacy clients still connecting

• Solution: Add “Block legacy authentication” condition, communicate modern client requirements

7. Best Practices

7.1 Deployment Strategy

• Phased rollout: Start with pilot groups and high-risk apps
• User communication: Educate users about new requirements and supported apps
• Monitoring period: Watch sign-in logs closely during initial weeks
• Fallback procedures: Maintain emergency access accounts and alternative methods

7.2 Policy Design

• Least privilege: Only apply controls where necessary for data protection
• User experience: Balance security with productivity requirements
• Regular reviews: Audit policies quarterly for effectiveness and user impact
• Integration testing: Verify APP and CA work together without conflicts

By implementing Conditional Access policies that require App Protection Policies, you create a robust defense for corporate data that works across managed and unmanaged devices. The key is careful planning, phased deployment, and continuous monitoring to ensure security without compromising user productivity.