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Getting Started with the Microsoft Intune Integration

  • Last Updated February 6, 2026

Topic

This article explains how to integrate Microsoft Intune with NinjaOne to import your devices. 

Environment

  • NinjaOne Integrations
  • Microsoft Intune
  • Microsoft Windows

Description

Use the Microsoft Intune integration in NinjaOne to identify the devices on the network and review saved jobs and their history. 

The Microsoft Intune device discovery process in NinjaOne supports multiple membership types that you can maintain in Microsoft Entra, including static (assigned) and dynamic rules. NinjaOne will deduplicate devices that exist in multiple selected Entra groups to prevent the creation of duplicate unmanaged devices in the console. To learn more about the data fields that are imported and displayed for unmanaged devices synced from Microsoft Intune, refer to NinjaOne Platform: Finding Discovered Devices.

View additional tutorials in our video library. 

Index

Select a category to learn more: 

Important Considerations

You may experience a delay when Microsoft Intune deploys applications. Some devices may only "check in" once every 24 hours, even if you run a manual sync. 

If you delete the NinjaOne agent deployment application from Microsoft Intune, NinjaOne will not detect this change and will continue to sync with Microsoft Intune. 

You must run a manual discovery job to sync devices that were added after the initial discovery run. We are working to improve this process in a future release. 

Grant Technicians Access to Configure Microsoft Intune

System administrators have access to the Microsoft Intune integration by default. To grant a technician access, you must select "Allow" for System → Configure Microsoft Intune on their account or role configuration page. 

Refer to User Permissions: Permission Options for more information. 

Enable Microsoft Intune in NinjaOne

To get started, you must enable the third-party application: 

  1. Go to Administration → Apps → Installed and click Add app. 
admin_apps_add app.png
Figure 1: Add the Microsoft Intune application in NinjaOne
  1. Find and select Microsoft Intune.
  2. On the application page, click Enable. 

Microsoft Intune Device Discovery

To start adding devices, click View Microsoft Intune discovery jobs to navigate to the Administration → Devices → Discovery page and perform the following steps. 

intune_view microsoft discovery jobs.png
Figure 2: Use Microsoft Intune to find devices
  1. Click Intune device discovery. 
discovery_intune device discovery.png
Figure 3: Intune device discovery
  1. Enter a unique identifier for Job name.
  2. Select the organization where the devices will be assigned. The Target organization drop-down menu will show all organizations in NinjaOne.
  3. Select the organization's location from the Target location drop-down menu.
  4. By default, the discovery process will automatically install the NinjaRMM agent onto the device. If you do not want this to occur, or if the agent has already been deployed through Microsoft Intune admin center, de-select the Deploy agent to discovered devices checkbox. To learn more about the NinjaRMM agent deployment in Microsoft Intune, refer to NinjaOne Agent Installation: Deploy via Microsoft Intune. If NinjaOne cannot automatically deploy the agent to the device, the system will create an unmanaged device account in the console. For more information about unmanaged devices, refer to Working with Unmanaged Devices in NinjaOne (ITAM).
  5. Click Sign in with Microsoft and follow the prompts to authorize NinjaOne with your Microsoft 365 account. Accept the request to grant permissions to NinjaOne. 
You must sign in with a system administrator role. 
intune device discovery and assign.png
Figure 4: Set up Microsoft Intune to sync data

After you click Accept, you will return to the NinjaOne Intune device discovery & assign configuration modal. You should now be able to view the Microsoft tenant name and Microsoft tenant ID fields populated with data. 

  1. Click Run Discovery. 

The modal will update to show the Run discovery tab, which lists all Entra Groups from your connected Microsoft account. 

  1. Select the checkbox for each group of devices you would like to assign to the organization and location. You can use the search field to find the Group by name. 
  2. Click Assign to set the connection and run the discovery. 
intune device discovery and assign_run discovery selection.png
Figure 5: Assign selected group

In Microsoft 365, you can go to Apps → Windows to find the "NinjaOne RMM" application. You may need to wait a few moments and refresh the page for changes to update. 

N1 app in M365 ex.png
Figure 6: Example of the NinjaOne RMM application in Microsoft (click to enlarge)

Resolve a "Pending" Account Status 

If you encounter any errors when attempting to log in to Microsoft during the discovery process, you may see "Pending" in the Status column. 

intune discovery pending.png
Figure 7: Microsoft Intune connection pending

To correct this issue, perform the following steps: 

  1. Select the checkbox next to the job name and then click Edit. 
edit intune discovery job.png
Figure 8: Edit the discovery job
  1. Click Re-authenticate with Microsoft. 
MI_intune device discovery_edit_reauthenticate.png
Figure 9: Re-authenticate your Microsoft account

Run a Manual Discovery to Sync New Devices

To run a manual discovery job and sync devices that were added after the initial discovery run, move your cursor over the job and click the ellipsis button. Then, select Run. 

For more information, refer to NinjaOne Platform: Finding Discovered Devices.

admin_run a discovery job.png
Figure 10: Run an ad hoc discovery job

Additional Resources

To learn more about device discovery with Microsoft Intune, refer to these guides:

FAQ

Next Steps