Yes. The multi-factor authentication (MFA) method used for your CUNY Login is separate from the MFA used for your CUNY email account in Microsoft 365 (and also different than the MFA used for your old college email account).
You may use the same authenticator app for both, but you must add each account as a separate entry in the app.
Be sure to use clear names for each system that requires MFA. For example, in Microsoft Authenticator or Google Authenticator, you can create distinct entries labeled “CUNY Login” and “CUNY Email.”
Learn more about CUNY Login MFA and CUNY Microsoft 365 MFA (email).