Coverage-dependent structural and electronic properties of Fe-phthalocyanine (FePc) molecules adsorbed on Ag(111) have been investigated by scanning tunneling microscopy/spectroscopy and density functional calculations. While spectra of single FePc molecules are dominated by a broad signature of Fe d orbitals, spectra of molecules in an ordered superstructure resolve spectroscopic contributions from individual d(z2) and d(xz)/d(yz) orbitals. Calculations suggest that an increased molecule surface distance in the superstructure and a change of the Ag(111) surface electronic structure cause the spectral changes, which are consistent with a partial electronic decoupling of the molecules from the substrate. A progressive evolution toward a gap around the Fermi level is observed for molecules on the first and second molecular layer.