Understandings of spatiotemporal dispersals of Homo sapiens onto the neotropical South American landscape and their environmental interactions during the late Pleistocene to late Holocene are being refined by multidisciplinary archaeological research. The Sabana of Bogota region in Colombia hosts a concentration of occupational sites, including Tequendama (13,525-2,330 and possibly until 815 cal BP) and Aguazuque (5,900-2,750 cal BP), that offer a view into local human paleoecology. Here, we conduct radiocarbon and stable isotope analysis (δ 13C, δ 18O and δ 15N) of humans and fauna from these sites, and reveal significant interregional differences in dietary patterns through time. Specifically, individuals from Tequendama exhibit predominantly C3 diets, while individuals from Aguazuque show evidence of early C4 consumption, likely maize, around 4,400-4,200 cal BP. Stable carbon and oxygen isotope data suggest environmental stability, with periodic deviations in aridity levels within a mosaic landscape. Our study highlights the complexity of human-environment interactions in the region and contributes to a broader understanding of isotopic variability.