How to Control App Access on Staff Devices Using Microsoft Intune

As businesses become more reliant on mobile and remote working, controlling access to apps on staff devices is no longer a luxury; it's a necessity. Whether your team is using smartphones, tablets, or laptops, making sure they only have access to authorised applications is key to maintaining data security and endpoint compliance.

If you’ve been asking yourself, “how to control app access on staff devices,” the good news is that Microsoft Intune provides a powerful and flexible set of tools to help manage access efficiently. In this blog, we’ll explore the techniques you can use within Microsoft Intune to have complete control over application access on company-managed or BYOD (Bring Your Own Device) endpoints.

Why Controlling App Access Matters

When staff have unfettered access to third-party apps or can download unapproved software, several risks emerge:

• Data Leakage: Sensitive company data might be saved or shared using insecure apps.

• Compliance Risks: Non-compliance with industry regulations due to the use of non-sanctioned apps.

• Security Threats: Malware or vulnerabilities introduced through unvetted applications.

• Reduced Productivity: Access to distracting or non-work-related applications.

Fortunately, Microsoft Intune helps overcome these challenges with a suite of policies and controls tailored to secure and manage application access.

Step-by-Step: How to Control App Access on Staff Devices with Microsoft Intune

1. Configure App Protection Policies

App Protection Policies (APP) help protect company data within approved applications, particularly useful in BYOD scenarios where devices aren’t fully managed. These policies ensure that data accessed via work applications is controlled, even without device-level control.

• Restrict copy/paste between apps

• Encrypt app data at rest

• Require PIN to access apps

• Wipe corporate data if the app becomes non-compliant

You can create protection profiles from Microsoft Intune by navigating to Apps > App protection policies and assigning them to user groups that need access restrictions.

2. Implement Mobile Application Management (MAM)

Mobile Application Management helps ensure that business applications are separated from personal data and applications on employee devices. With MAM, even if your staff brings their own devices, you can still control the apps they use for work without managing the complete device.

Set MAM policies to:

• Control which apps can access work data

• Block backup of company data to cloud storage (like iCloud or Google Drive)

• Deploy wipe commands for corporate data only

3. Use Conditional Access Policies

Conditional Access (CA) policies work with Microsoft Entra ID (formerly Azure AD) to ensure that access to apps depends on conditions such as user role, device compliance, location, or risk level.

For example:

• Only allow app access from compliant devices

• Deny access from unmanaged or jailbroken/rooted devices

• Prompt multi-factor authentication for high-risk logins

To configure, go to Microsoft Intune > Endpoint Security > Conditional Access and create policies aligning with your security needs.

4. Control App Deployment Through Managed App Store

Microsoft Intune allows admins to provide a curated set of applications users are permitted to install and use. Deploy only whitelisted apps through:

• Microsoft Store for Business (on Windows)

• Apple VPP (Volume Purchasing Program) for iOS/iPadOS

• Managed Google Play for Android

These integration channels ensure apps are pre-approved, automatically provisioned, and update-managed within Intune.

5. Create Device Compliance Policies

In addition to app-specific controls, robust device compliance policies can indirectly limit access. By marking devices as non-compliant if they don't meet certain criteria (e.g., OS version, encryption enabled), users won’t be able to use apps until they address those issues.

This adds an extra layer of assurance — only secure, up-to-date, governed devices can access corporate applications.

6. Monitor Access and Usage with Reporting

Intune's built-in analytics and reporting capabilities give organisations visibility into how apps are being used, what versions are installed, and what access control policies are applied. Use these tools to regularly audit access, adjust policies, and maintain compliance.

Best Practices to Enhance App Access Control

• Start with a baseline policy: Cover all users with minimum security requirements.

• Audit app usage: Remove unused or redundant app assignments frequently.

• Use least privilege access: Grant the minimum access necessary to perform tasks.

• Enforce app updates: Keep all apps patched against new vulnerabilities through update policies.

Final Thoughts

Knowing how to control app access on staff devices is crucial for maintaining data integrity and workplace productivity. Microsoft Intune offers a comprehensive toolkit that enables businesses to manage and secure application access across a variety of devices. From App Protection Policies to

Conditional Access, the right strategies will ensure staff are productive without sacrificing security.

If implementing Intune still feels overwhelming, Circuit Minds is here to help. As Microsoft 365 and Azure specialists, we guide businesses of all sizes through planning, implementing, and maintaining a secure and compliant endpoint ecosystem.

👉 Book a free consultation to learn how Circuit Minds can help you.