We study the influence of gravitational microlensing on the spectral line profiles originating from a relativistic accretion disc. Using the Chen & Halpern model for the disc, we show the noticeable changes that microlensing can induce in the line shape when the Einstein radius associated with the microlens is of a size comparable to that of the accretion disc. Of special interest is the relative enhancement between the blue and red peaks of the line when an off-center microlens affects the approaching and receding parts of the accretion disc asymmetrically. In an AGN formed by a super-massive binary in which the accretion disc is located around one of the super-massive companions (the primary), we discuss the possibility of microlensing by the secondary. In this case the ratio between the blue and red peaks of the line profile would depend on the orbital phase. We have also considered the more standard configuration of microlensing by a star-sized object in an intervening galaxy and find that microlensing may also be detected in the broad emission lines of multiply imaged QSOs. The changes observed in the line profile of Arp 102 B are taken as a reference for exploring both scenarios.