Persistence of top predators in protected areas requires healthy populations of prey species. Jaguars (Panthera onca) are top predators in the Caatinga dry forest, a xeric domain in northeastern Brazil. Poaching is a threat to populations of jaguar prey in the Caatinga, but it is still widely popular among locals. Here, we investigated molecularly identified jaguar scats to assess prey composition in a protected area where large prey has been heavily depleted or driven extinct by poaching. We also make direct comparisons between trophic niche width and mean prey size through a literature review. We show that over 90% of the diet of jaguars was comprised of prey under 5 kg, mainly armadillos. Furthermore, we found that the values of trophic niche width (2.21) and mean prey size (5.23 kg) in our study area are among the lowest ever described for jaguars in the literature. Our results demonstrated that jaguars are able to shift their diet to small prey when larger quarry is scarce. However, subsisting in such a stressful trophic position may lead to decreased levels of recruitment and low emigration rate. Breeding females would have difficulty raising cubs without abundant large prey. If jaguars are to persist in the Caatinga, effective actions to reduce poaching inside protected areas and corridors must be implemented. One of the most important jaguar populations in this domain inhabits our study site, and prey conservation is paramount for long-term persistence of this top predator in the Caatinga.