The family of phthalocyanine (Pc) is suitable functional molecules in the field of molecular electronics because of their thermal stability and the possibility to tune their structure, chemical, magnetic, and transport properties by means of different metallic cations within the Pc molecular cage. Here we report the depth dependent chemical composition and magnetization of iron phthalocyanine (FePc), cobalt phthalocyanine (CoPc) and binuclear (Co–Fe)-phthalocyanine [(Co–Fe)Pc] thin films grown on sapphire substrates by molecular beam epitaxy. The binuclear (Co–Fe)Pc films grown by coevaporation of pure FePc and CoPc exhibited a new structure (binuclear) which show drastically different conducting and magnetic properties. Using X-ray reflectivity (XRR) and polarized neutron reflectivity (PNR), we demonstrated that the structural changes in binuclear (Co–Fe)Pc films as compared to pure film is responsible for about three to four order reduction in resistivity and presence of ferromagnetism in this film at l...