The inner shell excitation of CuPc, NiPc, and H2Pc phthalocyanines at both C and N K-edges has been investigated theoretically by density functional theory calculations. The selected molecules allow one to study the effect on the spectra of the presence and the nature of the atom in the central cavity of the macrocycle. The individual characteristics of the spectra can be rationalized in terms of the position of the unequivalent C and N atomic sites, showing that sensible changes are present in the spectral features deriving from the N atoms directly bound to the atom at the center of the Pc macrocycle. The minor variations present in the spectral C 1s profiles of the phthalocyanines reflect the little perturbation experienced by the peripheral atomic sites.