We study the proton diffusion process in imidazole-based molecular crystals, which are new candidate materials for fuel cell membranes. These materials are characterized by hydrogen bonded networks of molecules, which provide viable routes for the long-range diffusion of protons. By the application of a recently developed, powerful technique to determine reaction pathways in complex systems, we are able to reproduce the diffusion process in the imidazole crystal and in the more complicated and rigid structure of imidazole 2-ethyleneoxide. Our results cast new light on the atomistic details of the molecular rearrangements sustaining the ionic diffusion.