The extent of pre-Columbian land use and its legacy on modern ecosystems, plant associations, and species distributions of the Americas is still hotly debated. To address this gap, we present a Holocene palynological record (pollen, spores, microscopic charcoal, SCP analyses) from Illimani glacier with exceptional temporal resolution and chronological control close to the center of Inca activities around Lake Titicaca in Bolivia. Our results suggest that Holocene fire activity was largely climate-driven and pre-Columbian agropastoral and agroforestry practices had moderate (large-scale) impacts on plant communities. Unprecedented human-shaped vegetation emerged after AD 1740 following the establishment of novel colonial land use practices and was reinforced in the modern era after AD 1950 with intensified coal consumption and industrial plantations of Pinusand Eucalyptus. Although agroforestry practices date back to the Incas, the recent vast afforestation with exotic monocultures together with rapid climate warming and associated fire regime changes may provoke unprecedented and possibly irreversible ecological and environmental alterations.