Topological insulators are a promising class of materials for applications in the field of spintronics. New perspectives in this field can arise from interfacing metal–organic molecules with the topological insulator spin-momentum locked surface states, which can be perturbed enhancing or suppressing spintronics-relevant properties such as spin coherence. Here we show results from an angle-resolved photemission spectroscopy (ARPES) and scanning tunnelling microscopy (STM) study of the prototypical cobalt phthalocyanine (CoPc)/Bi2Se3 interface. We demonstrate that that the hybrid interface can act on the topological protection of the surface and bury the Dirac cone below the first quintuple layer.