Microsoft Defender for Endpoint is a fantastic EDR, but its protection is only as good as its deployment and configuration. With Defender for Endpoint’s inclusion in enterprise licensing agreements, such as Microsoft 365 E5, organizations are more frequently moving to Defender for Endpoint as their primary EDR solution.
At Sevco, we’ve noticed while working with these organizations that for the security analyst responsible for its enterprise-wide health, “set and forget” is often a recipe for failure. Common configuration drifts and deployment gaps create significant and silent blind spots. Microsoft has written extensive troubleshooting documentation but the issue often is reliably identifying legitimate issues that require investigation from typical operations such as inactive users, offboarded devices, or even devices that are out of scope for Defender coverage.
Here are the five most common pitfalls we see managing Defender for Endpoint at scale.
Pitfall 1: Incomplete Coverage
The highest risk endpoint is the one you don’t know about. In dynamic environments with cloud instances, transient VDI, and multiple management systems (Intune, SCCM, Jamf), achieving complete deployment coverage with Defender is very difficult. Relying solely on the Defender device inventory is a mistake; you must identify the gaps between what is managed and what should be managed.
This gap is from devices that exist in inventory sources (Azure AD, on-prem AD), cloud provider consoles (Azure, AWS), or other management tools but have failed to onboard to Defender. Reasons include failed GPO/Intune policy application, network segmentation blocking access to onboarding URLs, or simply a broken deployment workflow for new assets.
How to Fix It:
- Establish Ground Truth: Systematically export device lists from your core sources:
- For AzureAD: Get-AzureADDevice Azure AD PowerShell cmdlet / Get-MgDevice Microsoft Graph PowerShell cmdlet
- For on-premise Active Directory: Get-ADComputer PowerShell cmdlet
- For Cloud compute instances: AWS/GCP/Azure CLI commands to list instances.
- Exports from other security agents (e.g., vulnerability scanners, other EDRs).
- Identify the Delta: Use a PowerShell or Python script to compare these lists against an export of your Defender for Endpoint device inventory, which you can obtain via the Graph API or the portal. The devices present in your source lists but absent from the Defender inventory are your immediate coverage gap.
- Remediate: Prioritize this delta list for investigation. Determine why the onboarding process failed and re-initiate it using the appropriate deployment package for that device type. Automate this reconciliation process to run weekly.
Pitfall 2: Incomplete Onboarding
A device appearing in the Defender portal does not mean it’s successfully onboarded! The onboarding process can stall, leaving the device in a state where it’s inventoried but not actually protected or reporting security data.
The Microsoft Graph API exposes several onboardingStatus values. Onboarded is the healthy state, any other Status value means the device is not protected by Defender:
- CanBeOnboarded: The device is known to Microsoft (often via Azure AD registration, Defender device discovery, or co-management) but the Defender sensor has not been successfully deployed and registered. This often points to a failed script or a policy that was targeted but never applied.
- Unsupported: The OS is incompatible (e.g., Windows 7 without ESU, an unsupported Linux kernel). Your deployment scripts should have logic to filter these out to reduce alert fatigue.
- InsufficientInfo: The state cannot be determined, which warrants investigation.
How to Fix It:
- Filter for Problem States: In the Microsoft 365 Defender portal, navigate to the Device Inventory and create a filter for Onboarding Status is not Onboarded.
- Troubleshoot Connectivity: For CanBeOnboarded devices, ensure they can reach the necessary URLs for the Defender for Endpoint service. Use Microsoft’s MDE Client Analyzer tool to diagnose connectivity or sensor issues.
- Verify Policy Application: For devices managed by Intune or GPO, verify that the onboarding policy has actually been applied to the endpoint. Check local event logs and registry keys (HKLM\SOFTWARE\Policies\Microsoft\Windows Advanced Threat Protection) to confirm the policy settings are present.
Pitfall 3: Inactive Sensors
A successfully onboarded sensor can still fail. A sensor that stops communicating is a critical blind spot, because it is reported as installed and Onboarded but is not actually being protected.
The sensor health state (DeviceHealthStatus) is a key indicator. Pay close attention to these states:
- Active: Healthy. The device is sending heartbeats and telemetry.
- Inactive: The device has not sent a signal for more than seven days. This could be a Critical finding if the agent is not functioning. You can compare activity in other sources to identify inactive devices that should be active.
- ImpairedCommunication: The MsSense.exe process is running but cannot reach its Command and Control (CnC) servers. This is almost always a network issue (proxy, firewall, VPN) blocking required Microsoft URLs.
- NoSensorData: The sensor is not sending telemetry, even if it’s sending heartbeats. This can indicate a performance issue or a conflict with other software.
How to Fix It:
- Check Sensor State: On a local machine, run the PowerShell cmdlet Get-MpComputerStatus and ensure AntispywareEnabled, AntivirusEnabled and RealTimeProtectionEnabled are all True.
- Enterprise-Scale Monitoring: In the Defender portal, regularly filter the device inventory for Health status is not Active. Prioritize Inactive and ImpairedCommunication. Look to confirm whether Inactive devices are active in other sources as this could indicate a broken agent.
- Troubleshoot with the Analyzer: For problematic devices, deploy and run the MDE Client Analyzer. It generates a detailed report of sensor health, connectivity checks, and event log analysis that will pinpoint the root cause of the communication failure.
- Network Path Verification: For ImpairedCommunication, verify that the device’s network path allows traffic to the URLs specified in the official Defender for Endpoint documentation.
Pitfall 4: Stale Protection
An active sensor is useless if its security intelligence is out of date. The Defender Antivirus engine relies on constantly updated signatures and behavioral models, old intelligence means old protection.
Monitor the DefenderAvStatus property for each device.
- NotUpdated: The Security Intelligence version is stale. This indicates the Defender AntiMalware engine isn’t up to date and a potential problem with the device’s update source, whether it’s Windows Update, WSUS, or SCCM.
- Disabled: Critical. The real-time protection engine is not running. This is often caused by a conflicting AV product being installed (even a remnant of a previous install) or a misconfigured policy.
- NotReporting: The AV engine’s state is unknown, which is a sign of a deeper sensor health problem.
How to Fix It:
- Force Updates Manually: For a single device, you can force a signature update from an elevated command prompt (“%ProgramFiles%\Windows Defender\MpCmdRun.exe” -SignatureUpdate -MMPC) or PowerShell (Update-MpSignature). This helps determine if the issue is with the update schedule or a fundamental connectivity problem.
- Audit Update Channels: Create reports in Defender or use the Graph API to find all devices where defenderAvStatus is NotUpdated. Investigate the update source for these devices. Check Windows Update logs (Get-WindowsUpdateLog) for specific error codes related to failed definition updates.
- Check for Conflicts: For Disabled devices, check for other security software. Run the Get-MpComputerStatus cmdlet and look at the AMServiceEnabled and AntispywareEnabled fields.
Pitfall 5: Siloed Data
The final pitfall is attempting to manage Microsoft Defender for Endpoint in a vacuum. The Defender portal provides a wealth of data about endpoints, but its true value is unlocked when you correlate it with data from other systems. Without this correlation, you can’t prioritize effectively.
Your CMDB, vulnerability scanner, and cloud inventory hold business context that Defender lacks. For example, knowing which Inactive sensor belongs to a domain controller, or which device with a Disabled AV engine has critical vulnerabilities and is internet-facing, is essential for risk-based prioritization. The Microsoft 365 Defender portal and its underlying Graph API are the sources for security posture, but they are not the source for business context.
How to Fix It:
- Leverage the Graph API: Do not rely on manual portal checks. Automate the extraction of device inventory and health data using the Microsoft Graph Security API.
- Correlate and Enrich: In your scripts or data platform, join the Defender data with asset information from your other sources using a common identifier like hostname or FQDN.
- Build Prioritized Workflows: Create queries that answer risk-based questions:
- “Show me all devices tagged as ‘Server’ in my CMDB with a Defender health status of Inactive.”
- “List all devices with ‘Critical’ vulnerabilities from Tenable that also have a Defender AV status of NotUpdated.”
This correlated view transforms raw data into actionable security intelligence.
The Automated Solution: From Manual Scripts to an Exposure Assessment Platform (EAP)
Manually performing this analysis across dozens of data sources and thousands of devices is unsustainable. The scripting is complex, the APIs change, and the process is inherently reactive. The Sevco Exposure Assessment Platform (EAP) addresses these issues.
Built on the foundation of Cyber Asset Attack Surface Management (CAASM), the Sevco platform automates the entire process described above. We aggregate and correlate asset data from your entire toolchain—including Microsoft Defender for Endpoint, Azure AD, your vulnerability scanner, and more—into a single, comprehensive, and accurate inventory.
Instead of running scripts to find gaps, Sevco gives you a real-time dashboard that visualizes these pitfalls. You can see your true Defender for Endpoint coverage, identify devices with unhealthy sensors, and correlate those findings with other risk factors like vulnerabilities and misconfigurations—all from a single interface.
If you’re tired of chasing gaps in your Defender deployments and want to move from reactive troubleshooting to proactive management, book a demo today!