We investigate the spectral evolution in different metal phthalocyanine molecules on NbSe2 surface using scanning tunnelling microscopy (STM) as a function of the coupling with the substrate. For manganese phthalocyanine (MnPc), we demonstrate a smooth spectral crossover from Yu-Shiba-Rusinov (YSR) bound states to spin-flip excitations. This has not been observed previously and it is in contrast to simple theoretical expectations. We corroborate the experimental findings using numerical renormalization group calculations. Our results provide fundamental new insight on the behavior of atomic scale magnetic/SC hybrid systems, which is important, for example, for engineered topological superconductors and spin logic devices.