We explore the impact of a millennium-long period of decreased rainfall during the transition from the Middle to Late Holocene on human diet and population dynamics in the northern neotropical Maya Lowlands. To do so, we use a nearby paleo-precipitation reconstruction to evaluate the timing of this period of reduced rainfall and compare those data to population proxies and stable isotopes of carbon and nitrogen from directly dated human bone spanning the interval of interest. Our results show that decreased precipitation coincided with archaeological and isotopic evidence for increasing reliance on maize as a dietary staple. Two rockshelter sites located in Southern Belize have produced a mortuary assemblage that spans the Holocene. These assemblages provide a unique opportunity to examine how early farmers during the transition to agriculture may have been affected by Middle to Late Holocene climate change. Between 5600 and 4200 cal BP lowland populations were already consuming significant amounts of maize reflected in proxies for the protein and the whole diet portions, suggesting the establishment of farming communities at least 800–2200 years before the emergence of public architecture. We demonstrate that increasing reliance on maize shows the resilience of farming populations to climate variability during this crucial period just prior to massive demographic change and the emergence of complex economic institutions.