The effect of annealing and cooling on the structural properties of thin cobalt films possessing either hcp(0001) or fcc(100) crystalline arrangement is studied on clean and carbonreconstructed W(110), respectively. The films grown on a clean W(110) crystal present a surface with hexagonal symmetry and undergo the well-known hcp−fcc structural transition upon annealing to temperatures higher than 700 K, while after cooling down to room temperature, the film is characterized by a laterally heterogeneous morphology featuring different stacking configurations. On carbide-covered W(110), Co grows, instead, in an fcc(100) arrangement with a high level of disorder, for which annealing leads to an improved crystalline order. Further annealing to above 900 K induces an irreversible transition from fcc(100) to hcp(0001) stacking via domain nucleation and growth on a micrometer scale. This recrystallization process is accompanied by a change in the film's chemical composition and magnetic structure. The excess carbon resulting from recrystallization leads to the growth of micrometer-sized graphene islands on top of the hcp regions.