The magnetic coupling of flexible metal phthalocyanine (MPc) thin films can be modified depending on the polymorphic form adopted by the crystals. A simple annealing procedure can switch the couplings from antiferromagnetic to ferromagnetic (MnPc) or paramagnetic (CuPc), opening up avenues for spintronic applications. Density functional and perturbation theories rationalize these trends and attribute the coupling mechanism to indirect exchange.