Sediment core PI-6 from Lake Petén Itzá, Guatemala, possesses an ~85-ka record of climate and environmental change from lowland Central America. Variations in sediment lithology suggest large and abrupt changes in precipitation during the last glacial and deglacial periods, and into the early Holocene. We measured stable carbon isotope ratios of total organic carbon and long-chain n-alkanes from the core, the latter representing a largely allochthonous (terrestrial) source of organic matter, to reveal past shifts in the relative proportion of C3–C4 terrestrial biomass. We sought to test whether stable carbon isotope results were consistent with other paleoclimate proxies measured in the PI-6 core, and if extraction and isotope analysis of n-alkanes is warranted. The largest δ13C variations are associated with Heinrich Events. Carbon isotope values in sediments deposited during the last glacial maximum indicate moderate precipitation with little fluctuation. The deglacial was a period of pronounced climate variability, e.g. a relatively warm and moist Bølling–Allerød, but a cool and dry Younger Dryas. Arid periods of the deglacial were inferred from samples with high δ13C values in total organic carbon, which reflect times of greater proportions of C4 plants. These inferences are supported by stable isotope measurements on ostracod shells and relative abundance of grass pollen from the same depths in core PI-6. Similar trends in carbon stable isotopes measured on bulk organic carbon and n-alkanes suggest that carbon isotope measures on bulk organic carbon in sediments from this lake are sufficient to infer past climate-driven shifts in local vegetation.