Hi Axel Pina,
I understand that you switched from legacy authentication to Conditional Access, but your Conditional Access policies are not applying to 39 users.
Since you recently switched from legacy/per-user MFA, you need to make sure that all of the users are set to "Disabled", since per-user MFA can override conditional access. You also need to make sure that the right scope for your policy is selected, as described here.
To troubleshoot this issue, you can check the Azure AD audit logs to see if there are any errors or issues with the policy. You can also use the WhatIf tool to get more detailed insights. See Troubleshooting sign-in problems with Conditional Access and Troubleshooting Conditional Access using the What If tool
If you have configured everything correctly and do not see additional errors, the issue might be because Conditional Access policies only apply to successful sign-ins. If a sign-in is successful, then the policies are evaluated to determine if the user should be able to access those resources.
If these suggestions and troubleshooting steps do not work, please share a screenshot of your policy with me so I can help determine if there is anything else that could be causing the issue.
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