Adding two-factor authentication to a website can be done using Google Authenticator and Twilio SMS. This method requires a shared secret between the user's device and the server, which is stored on the user's account page. The user scans a QR code with their device or enters their phone number to receive an SMS with the TOTP code. If the entered token is valid, two-factor authentication is enabled for the user's account. This process can be automated by using Google Authenticator and Twilio SMS, which provides a secure way for users to authenticate themselves.