Windows Server 2016 comes standard with built-in Anti-Malware called Windows Defender like Windows 10 Client. And per default, Windows Defender is active and has also turned on Real-Time Protection by default. In Windows Server 2016 Desktop Experience you can disable and configure Windows Defender using the UI or PowerShell, in the Windows Server 2016 Core version or on Nano Server you only have PowerShell available. Here are some quick command how you can do this:

Check the Windows Defender Configuration and Settings:

Turn off Windows Defender Real-Time Protection using PowerShell

Turn onWindows Defender Real-Time Protection using PowerShell

Add a File path exclusion:

Add process exclusion

 

I hope this helps you to easily configure Windows Defender on Windows Server 2016. Btw. This also works on Windows Defender on Windows 10.