Windows Intune will steal focus and prompt users to reboot after installing updates that requre reboot.

There are some ways to manage this:
1. You may give the users more time before the reboot (maximum30 mins)
2. You may disble installation of updates that require reboot
3. Enable restart later with a 60 minutes delay.

To enact one of these policies go here:
Navigate to policy

Policy management

Create a New policy

Choose “Windows Intune Agent Settings” and click “Create Policy”

Name the policy e.g. “Restart delay”
Give it a description (delayed restart by 30 mins, all Clients)

Click updates in the left corner

Here are the update options:

Windows Intune Agent Update Options

Now notice the: “Allowed logged on users to Control Windows Intune Restart”
Should be set to YES
In the other boxes you may set the time to max in order to steal minimal of focus with the restart prompt Box.

Now, save the policy and deploy it to all computers , or just a group of admins
Click “Save Policy”
and check computers to deploy the policy on: