Your Intune policies are the backbone of how Microsoft Entra ID enforces identity-based access and device compliance. But they’re not automatically protected by Microsoft. Losing them can break Conditional Access, device trust, and compliance enforcement across your tenant. In this blog, we’ll explore what these policies actually control, why they’re so critical, and how third-party protection like Veeam Data Cloud for Microsoft Entra ID keeps everything secure and recoverable.
TL;DR
- Intune policy objects live inside Entra ID, linking device compliance, app protection, and access control
- They’re not automatically backed up, meaning accidental deletions or misconfigurations can cause major outages
- Losing these policies can instantly block user access to Teams, Outlook, or SharePoint and weaken identity-based security
- Native exports and scripts don’t provide full restore capabilities or version history
- Veeam Data Cloud for Microsoft Entra ID automates backup and recovery, capturing complete policy relationships and assignments for fast, reliable rollback
Why Intune Policy Backup Matters
If you’ve ever set up Conditional Access or device compliance rules in Microsoft Entra ID, you’ve already relied on Intune policy data, whether you realized it or not. Every configuration profile, compliance rule, and app protection setting stored in Intune is also an Entra ID object that defines how users and devices interact with your organization’s data.
The catch? The Microsoft Entra ID Shared Responsibility Model states that Microsoft’s responsibility is the uptime of the service, not the recovery of your configurations. That means if a policy is deleted, corrupted, or overwritten, there’s no built-in safety net. Losing just one of these objects can disrupt device access, revoke Conditional Access permissions, and create serious security gaps.
Understanding Intune Policy Objects in Entra ID
Before we talk protection, it helps to know what’s actually at stake. Intune policies are stored as objects in Entra ID that work together to maintain device trust and access control. Some of the most important include:
- Device compliance and configuration policies
These set rules for encryption, OS version, password strength, and device health. Their results are evaluated in Entra ID to determine whether a user’s device can sign in.
If one of these is lost or corrupted, compliant devices may instantly appear “unhealthy,” blocking user access
- Conditional Access links
Entra ID uses Intune compliance data to enforce access decisions. If the link between these systems breaks, healthy devices can be locked out entirely
- App protection and assignment policies
These define which apps can handle corporate data and enforce actions like blocking copy-and-paste or requiring PINs for access. Losing an assignment means users could move data between personal and corporate apps without restriction
- Role-based access control (RBAC) and group assignments
These govern which admins can create or modify policies, and which user groups receive them. When these vanish or change unexpectedly, your entire security posture can shift overnight
All these configurations are part of Entra ID’s control plane, meaning that even though you interact with them through the Intune portal, their dependencies and permissions live inside Entra ID itself.
The Hidden Risk Behind Configuration Changes
Even the most organized IT teams deal with configuration drift. Here’s what can go wrong:
- Human error: An admin deletes or overwrites a policy during cleanup
- Automation gone wrong: A Graph API script pushes the wrong configuration to production
- Testing mishaps: A lab policy is assigned to live users
- Malicious edits: A compromised account intentionally disables compliance checks
A Quick Example
Picture this: Your remote workforce depends on Intune compliance policies to access Teams, Outlook, and internal VPNs. One morning, an admin unintentionally edits a compliance rule that checks for device encryption. Suddenly, thousands of devices are flagged as non-compliant, and Conditional Access blocks everyone from signing in.
Without a backup, IT scrambles to recreate the configuration from scratch, reassign policies, and reconnect Conditional Access links. It’s not just hours of downtime — it’s lost productivity, frustrated users, and potential audit risk.
Intentional Threats and Malicious Misconfigurations
As mentioned in our 6 Reasons for Microsoft Entra ID Backup white paper, not all risks to Intune and Entra ID policies come from accidents. In many modern breaches, attackers target identity and endpoint controls directly. According to the 2024 Microsoft Digital Defense Report, there are over 600 million identity-based attacks every day. Once a bad actor gains privileged access, altering Intune policy objects becomes a powerful way to weaken security without triggering immediate alerts.
A malicious edit or deletion can:
- Disable device compliance checks, making unpatched or unencrypted devices appear “healthy”
- Remove app protection policies, exposing corporate data in unmanaged apps
- Change RBAC permissions or group assignments, giving the attacker broader administrative reach
Since Conditional Access decisions rely on Intune’s “device is compliant” signal, tampering with these policies breaks the trust chain between devices and Entra ID. The result can be unauthorized access, data exposure, and large-scale downtime before IT even detects the change.
That’s why protecting these policy objects with automated backup and change detection isn’t just about recovery, it’s about maintaining security integrity in the face of intentional threats.
Why Native Options Fall Short
Microsoft’s export tools and Graph API scripts help with documentation, but not with protecting critical data. This can leave critical gaps in your protection strategy, as they:
- Require manual setup and ongoing maintenance
- Don’t capture full dependencies or assignment data
- Lack version control and point-in-time rollback
- Offer no protection for deleted or corrupted Entra ID objects
In short, Microsoft works to keep your service online, but you’re responsible for keeping your configurations recoverable.
The Veeam Approach
Native tools can document your configurations, but they don’t protect them. Veeam Data Cloud for Microsoft Entra ID offers protection for your critical Entra ID objects and Microsoft 365 in one unified SaaS experience, designed to simplify data resilience while protecting your organizations information and identities.
Veeam Data Cloud delivers:
- Purpose-built protection and recovery for Intune and other critical Entra ID objects
- Comprehensive Microsoft SaaS protection that extends to your Microsoft 365 workloads
- All built in a secure, unified SaaS platform
Final Thoughts
As organizations depend more on Intune and Entra ID to manage users in their environments, policy data has become mission-critical. Losing even one key configuration can lock out users, disable protection policies, and interrupt business operations.
With Veeam Data Cloud for Microsoft Entra ID, you can safeguard these policies automatically and recover them instantly when it matters most. It’s the difference between reacting to an outage and preventing one altogether.
Learn more about our Next-gen Data Resilience for Microsoft 365 and Entra ID.