Understanding Microsoft Intune Security Baseline: An In-Depth Guide Based on Real-World Experience

As organizations increasingly rely on cloud-based management tools, Microsoft Intune has become a pivotal part of managing device configurations, ensuring security, and enforcing compliance across various platforms. One of the most crucial aspects of Intune security management is the Security Baseline Policies. These policies, which are predefined sets of security settings provided by Microsoft, help ensure that devices comply with best security practices. However, as I’ve learned through firsthand experience, security baselines can sometimes present challenges, especially when they inadvertently block applications or cause issues with device behavior. In this article, I will share my experiences and insights on working with Intune Security Baseline Policies, troubleshooting common issues, and providing practical solutions for effective management.


What Are Intune Security Baseline Policies?

Security baselines in Intune are a set of predefined security configurations based on industry standards and best practices, aimed at ensuring the security of devices and data within an organization. These baselines cover key areas like:

  • Antivirus protection (Windows Defender)
  • App control and restrictions
  • Exploit protection
  • SmartScreen settings
  • Account lockout and password policies

By applying these security baselines, organizations ensure that their devices are configured securely without needing to manually configure each individual setting. However, as I’ll explain, there are challenges that can arise when these settings conflict with certain software or device configurations.


Common Challenges with Security Baseline Policies

In my experience, when security baseline policies are deployed across a broad range of devices, they sometimes cause unintended consequences. One of the primary concerns that often comes up is the blocking of legitimate applications. This can occur for several reasons:

1. Conflicts with Existing Applications:

Some applications may not be fully compatible with specific settings in the security baseline. For example, Windows Defender Application Control (WDAC) or Exploit Protection can block legitimate applications if they are not whitelisted or recognized by these security measures.

2. Overreaching Settings:

Some security settings may be too restrictive, such as SmartScreen filtering or Windows Defender Antivirus policies, which could block an application or even certain functions on a device without providing clear feedback. This can cause productivity disruption and lead to confusion among users.

3. Misalignment with Business Requirements:

Certain security configurations might not align with the specific needs of the business or users. For instance, an enterprise might rely on third-party applications that conflict with Intune's predefined settings, or have use cases where certain security measures need to be relaxed temporarily.


How to Exclude Applications from Security Baselines

While these security policies are critical, there are times when you need to exclude specific apps from being impacted by these baselines. The challenge comes when you need to strike a balance between enforcing security while also ensuring that legitimate business applications run without issues. Based on my experience, the most effective way to handle this is to exclude applications from specific security features or customize the security baseline settings.

Steps to Exclude Applications:

  1. Go to Intune Portal:
  2. Navigate to Security Baselines:
  3. Adjust or Exclude:
  4. Deploy Updated Policies:


What to Do When Security Baseline Policies Block Genuine Applications

Even after exclusions and modifications, if security baselines still block applications or functionality, it’s important to consider additional troubleshooting steps. Here’s a list of what I typically do when facing such issues:

1. Review the Impacted Policies:

Sometimes it’s not just one policy but a combination of settings in the baseline that’s causing the problem. I recommend going through each security policy, such as Windows Defender Antivirus, Exploit Protection, or App Control, and determining which one might be preventing the application from running.

2. Use Logging and Reporting:

  • Utilize Microsoft Defender for Endpoint’s logs to understand exactly which part of the security baseline is blocking the application. This can often help pinpoint the exact policy causing the issue.
  • You can also review logs from the Intune portal, where you can see the deployment status and check for failed policy applications.

3. Modify or Relax Security Policies Temporarily:

Sometimes, if it’s critical to run a specific application, I temporarily relax or disable certain baseline settings on a small group of test devices to ensure the application functions properly. This helps confirm the cause and allows you to decide whether the policy needs an exemption.


Challenges with Re-enrollment and System Repair

In some cases, after applying or adjusting security baselines, devices may still face issues with policies not being applied properly. During my work with Intune, I found that the only way to completely clear security baseline settings was to reenroll the device in Intune or perform a system repair (using tools like Windows Autopilot Reset or In-place upgrade).

Why Re-enrollment and System Repair Work:

  • Re-enrollment forces Intune to apply the latest device management policies and clear out old or conflicting configurations. This often clears up issues where security baseline settings were either applied incompletely or in conflict with other settings.
  • System repair or reset can also remove corrupted configurations at the local system level, which might not be cleared by Intune alone. This step essentially resets the local device settings to default, allowing Intune to reapply security policies without the interference of previous configurations.

Best Practice for Preventing These Issues:

Before applying security baselines broadly:

  • Test on a small group of devices to see how the baseline interacts with your applications.
  • Use Windows Autopilot to manage device resets or repairs.
  • Regularly monitor the Device Compliance Status in Intune to track any non-compliance issues early on.


Best Practices and Lessons Learned

From my experience working with Intune security baselines, here are some best practices:

  1. Test Before Deployment: Always test security baselines on a subset of devices before rolling them out to the entire organization to avoid unexpected disruptions.
  2. Use Exclusions Wisely: Be selective about which apps or features to exclude from security baselines. Overuse of exclusions can reduce the effectiveness of security settings.
  3. Regular Monitoring: Continuously monitor devices through Intune reporting and Microsoft Defender to identify potential policy conflicts and resolve them promptly.
  4. Leverage Device Grouping: Group devices logically (e.g., by department or user role) and apply tailored security baselines to ensure that policies are appropriate for each device’s use case.
  5. Re-enrollment and Repairs as Last Resort: Only resort to re-enrollment or system repair when all other troubleshooting methods have failed, as these processes can cause temporary disruption.


Conclusion

Intune security baselines are an essential tool for ensuring the security of your organization’s devices, but they can present challenges, especially when they block legitimate applications. Through my experience, I've learned that these issues can be resolved by fine-tuning security settings, using exclusions, and carefully monitoring the impact of security policies on devices.

If you encounter persistent issues, remember that re-enrollment or system repair may be necessary to fully reset and clear conflicting security settings. As long as you follow a structured approach—testing, monitoring, and selectively applying policies—security baselines can provide robust protection without hindering productivity.

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