A method and system for compensating for the effect of phase drift in a data sampling clock during data transfer between sub-systems of an electronic device. The sub-systems of the electronic device transfer data frame by frame. Each frame includes multiple data windows. Each data window includes multiple data bits. The method includes sampling each of the one or more data bits of a data window at one or more early instances, a prompt instance, and one or more late instances. Further, the method includes calculating the phase-error value of the sampled data window, based on the data sampled. Furthermore, the method includes compensating for the effect of phase drift in the data sampling clock, based on the calculated phase error value.