Lake sediments are unique archives of human environment interactions. Lake Prespa is one of the oldest lakes in Europe, lying in the southwestern Balkans and thus on a possible dispersal route of anatomically modern humans from Africa. In this study, we investigated the effects of climate, vegetation and human activity on fire over the last 92,000 years in this region. Sediment samples were taken from Lake Prespa, and nearby Lake Ohrid for comparison of the regional relevance, and analyzed for benzene polycarboxylic acids as markers for burned organic carbon residues (black carbon, BC). Peaking contents of BC (up to 1 g BC kg−1 sediment) coincided with warm and humid phases, when forests expanded at marine isotope stages (MIS) 5 and 1. During the colder and more arid climates of MIS 4 and 2, BC contents were lowered by a factor of 10, with a distinct minimum during the Last Glacial Maximum (0.07 g BC kg−1). The ratio of pentacarboxylic acid to mellitic acid (B5CA/B6CA) declined from 1.2 at MIS 5 to values of 0.3 at MIS 2, confirming a change in fire regime. Overall, BC contents peaked at cycles of solar radiation, vegetation composition and fuel availability, and thus correspond to the BC signal of other environmental archives. However, in the Late Holocene and as a result of human sedentary settlement, BC production increased, independent of decreasing insolation forcing.