Secondary doping of polyaniline (PANI) was explained by a change in the conformation of the polymeric chains from a coil-like to an extended structure, leading to an increase in the conductivity and in the crystallinity of polyaniline doped with functionalized organic acids. In this work, resonance Raman spectroscopy is used to characterize the secondary doping process aiming to understand the transformations in the different types of charged segments. Raman results give complementary data about the secondary doping process showing that together with the structural change of the polymeric chains there is also a chemical transformation of quinoid segments into semiquinone units. This fact was put in evidence by the careful analysis of Raman spectra at different excitation lines where different vibrational modes of chromophore groups are enhanced. This phenomena was also characterized by electron spin resonance (ESR) measurements that evidences an increase in the number of spins of PANI/CSA samples after the secondary doping process. Experimental results obtained by both techniques, resonance Raman spectroscopy and ESR, indicate the transformation of diamagnetic quinoid segments into radical cation semiquinone units.