In the present paper, we report a detailed analysis of the fluence-dependent conformational and structural changes induced in the polypyrrole nanofibers (PPy NFs) upon swift heavy ion (SHI) irradiation. PPy NFs, synthesized using a cationic surfactant cetyltrimethylammonium bromide-assisted micellar polymerization technique, have been irradiated with 90 MeV O7+ ions at normal beam incidence with fluence varying from 3×1010 to 1×1012 ions/cm2 using a 15UD Pelletron accelerator under ultra-high vacuum. X-ray diffraction studies reveal a decrease in the domain length and an increase in the strain upon SHI irradiation. A decrease in the integral intensity upon SHI irradiation indicates the amorphization of the material. Micro-Raman (μR) studies confirm amorphization of the PPy NFs and also show that the PPy NFs get de-doped upon SHI irradiation. μR spectroscopy also reveals a benzenoid to quinoid transition in the PPy chain upon SHI irradiation.