We present isotopic data from mammalian megafauna from the Jirau Paleontological Site (Itapipoca, Ceará State, Brazil) and Rio Miranda (Mato Grosso do Sul State), both located in the Brazilian Intertropical Region, dating to the Mid–Late Holocene. The isotopic composition (δ13C) of eight tooth fragments was determined for the following taxa: E. laurillardi, N. platensis, T. platensis, S. populator, X. bahiense, and P. major. Results indicate that the herbivorous taxa had mixed diets, consistent with deciduous to semi deciduous forest and wooded savannah environments. S. populator likely preyed upon herbivores with mixed diets and inhabited wooded savannahs. E. laurillardi, N. platensis, and T. platensis exhibited generalist feeding behavior with a high proportion of C₃ plants in their diet, associated with the fragmentation and reduction of open environments (savannah and wooded savannah) and the concurrent expansion of forested areas during the Holocene Climatic Optimum. X. bahiense and P. major exhibited browser-type diets in Itapipoca, suggesting adaptation to the expansion of deciduous and semi deciduous forests during the Holocene Climatic Optimum. By comparing isotopic data with paleoecological, palynological, and paleobiogeographical evidence, we infer that the Intertropical Region represented one of the last environmental refuges for extinct meso- and megamammal faunas during the Holocene.