A 50,000-year-old sediment core record from Laguna Chaplin is reanalyzed to explore potential paleoecological methods to detect the extent of pre-Columbian disturbance in the Bolivian Amazon. High-resolution (sub-centennial) macrocharcoal data are analyzed using statistical algorithm software including Regime Shift Detection and CHAR Analysis to detect changes in past fire regimes. These data are compared with existing charcoal records from throughout the Bolivian lowlands to provide a regional scale context of past biomass burning. During the mid-Holocene, changes in precipitation are the dominant driver of fire activity and biomass burning at Laguna Chaplin and across the Bolivian lowlands. During the late Holocene, increased fire activity across ecosystems ranging from fire-adapted to fire-intolerant forests is attributed to the apex of pre-Columbian activity. These data suggest human-caused ignitions during the late Holocene are the driving factor of regional scale fire activity in the Bolivian lowlands. After ca. 650 cal yr BP, there is an increase in biomass burning and fire frequency synchronous with the expansion of Moraceae/Urticaceae pollen (>50%) at Laguna Chaplin. This occurs during the time-transgressive southward expansion of the rainforest boundary, during the apex of pre-Columbian activity in the region. The increase in biomass burning at Laguna Chaplin is reflected at other sites in the region with known human occupation histories. The presence of Zea mays ca. 970 to 170 cal yr BP indicates maize cultivation is practiced in the immediate vicinity surrounding Laguna Chaplin. The simultaneous increase in fire activity with the expansion of the less flammable humid rainforest vegetation suggests human fire management practices. These data are interpreted as the use of frequent, low severity, human-caused fires to clear the croplands from encroaching rainforest vegetation. Despite evidence of pre-Columbian fire management during the late Holocene, vegetation and fire data indicate the extent of human-landscape modification and fire management at Laguna Chaplin, is not enough to inhibit the climate-driven regional forest expansion of the savanna-rainforest ecotonal boundary to its most southern extent in the last 50,000 years. This study demonstrates the utility of applying a multi-proxy, high-resolution paleoecological method to disentangle climate and pre-Columbian disturbance in the Bolivian Amazon.