Welcome to the Windows Autopatch Community!

Hi ambarishrh !
No you absolutely can still use Windows Autopatch if you have Conditional Access. However, conditional access policies will block Windows Autopatch service accounts from connecting to your tenant if the accounts are not excluded. As such, part of the enrollment process includes excluding our service accounts from your conditional access policies. For more information on how we handle this, check out our public docs on this: https://docs.microsoft.com/en-us/windows/deployment/windows-autopatch/prepare/windows-autopatch-fix-issues#conditional-access-policies