As far as I know, Windows Defender does not perform any background scheduled scanning.
You will get a notification from Windows Defender if a scan is required, or after cleaning WD files with CCleaner.
It may be the Automatic Maintenance during idle times, such as installing updates, disk defrag/trim or anything else. You can change the settings from the Action Center, via the System Tray or Control Panel.
If you check the Task Manager during this time, what processes do you see occupying the CPU the most? svchost.exe, Trustedinstaller.exe or other?