For the first time resonance Raman, X-ray absorption near edge structure (XANES) of Fe, Cu and N and electronic paramagnetic resonance (EPR) techniques were employed to characterize the complexes formed by the interaction of Fe(III), Cu(II) and Zn(II) with polyaniline (PANI), in emeraldine base form (EB-PANI). The formation of semiquinone segments (radical cation) upon coordination of Cu(II) and Fe(III) to EB-PANI were undoubtedly demonstrated by resonance Raman spectroscopy. The characteristic doublet band at ca. 1330 cm−1 attributed to νCN+• is observed. Through Cu and Fe XANES spectra, no change in the metal ions oxidation state after PANI doping is observed. The EPR spectra of Cu-PANI and Fe-PANI are dominated by metal cation signal showing a broad signal for Cu(II) at giso = 2.138 and a typical low spin signal of Fe(III) at g = 4.421 and 1.903. The presence of radical cations segments is confirmed in Zn-PANI complex both through the very sharp EPR signal at g = 2.004, and the characteristic radical cation resonance Raman spectrum. In addition, thermogravimetric data of Cu-PANI and Fe-PANI show a remarkable decrease in the polymer stability both in air and in nitrogen atmosphere.