Stable isotopes (δ 13C and δ 15N) have been widely used to track cephalopod habitat, migration and trophic structure. In this study, we analyzed the δ 13C and δ 15N values in 245 Dosidicus gigas beaks collected during 2009–2010 and in 2013 off Peruvian Exclusive Economic Zone (EEZ) waters. High individual variation in beak stable isotopes was shown with values ranging from −19.4‰ to −15.8‰ for δ 13C and from 5.0‰ to 15.1‰ for δ 15N. A generalized additive model (GAM) showed that latitude, mantle length and distance to shelf break significantly described the isotope variation with deviance ranging from 16.6% in δ 13C to 36.3% in δ 15N. Large variability in beak δ 13C values for a given size and sampling station indicated that D. gigas off the Peruvian EEZ waters migrate in different ways when they occupy a large range of habitats for their ontogeny. Low baseline δ 15N values suggested that spatial changes in diet trophic level may be the main determinative factor in beak δ 15N variation. We conclude that high variability in beak δ 15N values for a given set of explanatory variables indicated that D. gigas is an opportunistic predator with highly diverse dietary habitats. This study further develops our knowledge of the life history of D. gigas in such a highly dynamic region.