The thermal behavior of PANI nanofibers doped with β-naphthalenesulfonic acid (β-NSA) was investigated and their morphological and structural changes after heating were monitored by SEM, XRD and Raman techniques, respectively. By using electron-scanning microscopy it is possible to verify that the nanofiber morphology is stable and no polymer degradation is observed in thermogravimetric (TG) data up to 200 °C. Nevertheless, the heating promotes the formation of cross-linking structures (phenazine and/or oxazine-like rings), that is clearly demonstrated by the presence of bands at ca. 578, 1398, and 1644 cm−1 in resonance Raman spectra of heated PANI–NSA samples. The most important consequence of the formation of cross-linking structures in PANI–NSA samples is that these samples retain their nanofiber morphology upon HCl doping in contrast to PANI–NSA nanofibers without heating.