Tungsten nanofibers are recognized as biologically potent. We study deviations in molecular composition between normal and digestive gland tissue of WOx nanofibers (nano-WOx) fed invertebrate Porcellio scaber (Iosopda, Crustacea) and revealed mechanisms of nano-WOx effect in vivo. Fourier Transform Infrared (FTIR) imaging performed on digestive gland epithelium was supplemented by toxicity and cytotoxicity analyses as well as scanning electron microscopy (SEM) of the surface of the epithelium. The difference in the spectra of the Nano-WOx treated and control cells showed up in the central region of the cells and were related to lipid peroxidation, and structural changes of nucleic acids. The conventional toxicity parameters failed to show toxic effects of nano-WOx, whereas the cytotoxicity biomarkers and SEM investigation of digestive gland epithelium indicated sporadic effects of nanofibers. Since toxicological and cytological measurements did not highlight severe effects, the biochemical alterations evidenced by FTIR imaging have been explained as the result of cell protection (acclimation) mechanisms to unfavorable conditions and indication of a nonhomeostatic state, which can lead to toxic effects.