This study provides information about the diet across geographic areas and throughout ontogeny and sex of two coastal and commercial batoid species in Peru (Chilean eagle ray Myliobatis chilensis and Pacific guitarfish Pseudobatos planiceps). Data was collected in the central coast (13°30′S to 14°30′S; Pisco district, Lima) and in the northern coast (13°12′S to 13°49′S; San Jose district, Lambayeque) off Peru during the second semester of the years 2015 and 2016 (i.e., winter and spring) in an El Niño event. A total of 357 stomach contents were analyzed in northern and central Peru with different oceanographic and ecological conditions. In the central coast, M. chilensis showed a high trophic position (tertiary consumer) due to its high consumption of Peruvian anchoveta (Engraulis ringens), while P. planiceps had a lower trophic position (secondary consumer) and a less specialized diet of benthic invertebrates (i.e., crustaceans and mollusks) and pelagic fish (e.g., E. ringens). In the northern coast, both species preyed mainly upon benthic invertebrates and to a lesser degree on fish; therefore, their trophic position was lower. Dietary variation was influenced by species, geographic location, and ontogeny. The diet variability between geographic locations shows insights of these batoids’ trophic plasticity and opportunistic feeding behavior in response to differences in the local prey availability, an effect that may be amplified during the El Niño–Southern Oscillation (ENSO). The spatial variation in this species diet may indicate that they play different ecological roles in distinct environments. This study contributes to the scarce literature about batoids’ ecology in the southeast Pacific Ocean and presents novel information on habitat-specific diet composition.