Scanning tunneling spectroscopy (STS) has become a key tool for accessing properties of organometallic molecules adsorbed on surfaces. However, the rich variety of signatures makes it sometimes a difficult task to find out which feature is intrinsic to the molecule, i.e., relevant for a metal–ligand interaction or related to the interaction of the molecule with the substrate. Here we study the prototype covalent self-assembly of FePc and probe how electronic/magnetic properties at the local scale change as a function of temperature-induced step-by-step assembly, starting from TCNB (1,2,4,5- Tetracyanobenzene) molecular and Fe atomic precursors. Intermediate complexes with tetra-coordinated Fe atoms are then used both, as synthons for the FePc and as identifiers of specific features of the STS. As observed by STS and confirmed by spin-polarized DFT calculations, the occupied dπ states of Fe are present in both the FePc and Fe(TCNB)2 on Au(111). The main difference appears in the dz2 states, which play a key role in magnetism as confirmed by the presence/absence of the Kondo resonance. A comprehensive picture is obtained by following with STS the hybridization of the dz2 orbital of Fe to various substrates (Cu, Au and Co). Finally it is demonstrated that FePc units can be created by on-surface polymerization from the Fe(TCNB)2 network upon thermal annealing.