Hi @berketjune2012 ,
Yes, the antivirus policies are controlled from the Endpoint security policies. This is noted here: https://learn.microsoft.com/en-us/mem/intune/protect/endpoint-security-antivirus-policy
If servers are not onboarded to Intune, they cannot have endpoint security policies pushed to them since these are a feature of Intune. https://learn.microsoft.com/en-us/mem/intune/protect/endpoint-security
Let me know if this addresses your question.
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