Once MFA is enabled for your account, you will still use the magic link login process. However, after this step you will be asked to enter the verification code generated by your authenticator application. From here you will be logged in.
Please note: there is a two-minute window from the moment you open your magic link to enter your MFA verification code upon login. If you take longer than two minutes to enter the code, you must request a new magic link and repeat the login process.