Embodiments provide methods and systems for analyzing device behavior data in multi-factor authentication (MFA) process. The method includes receiving, by a server system, a request in association with a payment transaction between a cardholder and a merchant. The request includes a cardholder identifier and information of a successful verification of a user input entered by the cardholder to perform MFA of the payment transaction. The method includes identifying user profile data stored in a database based on the cardholder identifier. The user profile data includes information of a plurality of registered user devices associated with the cardholder. The method includes performing device behavioral analysis of one or more user devices. The method includes generating an MFA token associated with the payment transaction based on the device behavioral analysis. The method includes transmitting the MFA token for authorizing the payment transaction to a payment server associated with a payment network.