In this paper, we study the phenomenon of quantum interference in the presence of external gravitational fields described by alternative theories of gravity. We analyze both non-relativistic and relativistic effects induced by the underlying curved background on a superposed quantum system. In the non-relativistic regime, it is possible to come across a gravitational counterpart of the Bohm–Aharonov effect, which results in a phase shift proportional to the derivative of the modified Newtonian potential. On the other hand, beyond the Newtonian approximation, the relativistic nature of gravity plays a crucial rôle. Indeed, the existence of a gravitational time dilation between the two arms of the interferometer causes a loss of coherence that is in principle observable in quantum interference patterns. We work in the context of generalized quadratic theories of gravity to compare their physical predictions with the analogous outcomes in general relativity. In so doing, we show that the decoherence rate strongly depends on the gravitational model under investigation, which means that this approach turns out to be a promising test bench to probe and discriminate among all the extensions of Einstein’s theory in future experiments.