The Amazon Rainforest Ecotone (the ARF-Ecotone) of the southwestern Amazon Basin is a transitional landscape from tropical evergreen rainforests and seasonally flooded savannahs to savannah woodlands and semi-deciduous dry forests. While fire activity plays an integral role in ARF-Ecotones, recent interactions between human activity and increased temperatures and prolonged droughts driven by anthropogenic climate change threaten to accelerate habitat transformation through positive feedbacks, increasing future fire susceptibility, fuel loads, and fire intensity. The long-term factors driving fire in the ARF-Ecotone remain poorly understood because of the challenge of disentangling the effects of prolonged climatic variability since the Last Glacial Maximum (LGM; ~24,000 to 11,000 cal BP) and over 10,500 years of human occupation in the region. To investigate this issue, we implement an interdisciplinary framework incorporating multiple lake sediment cores, with varying basin characteristics with existing regional palaeoclimatological and archaeological data. These data indicate expansive C4 grasslands coupled with low fire activity during the LGM, higher sensitivity of small basins to detecting local-scale fire activity, and increased spatial diversity of fire during the Holocene (~10,500 cal year BP to the limit of our records ~4,000 cal year BP), despite a similar regional climate. This may be attributed to increased human-driven fire. These data raise the intriguing possibility that the composition of modern flora at NKMNP developed as part of a co-evolutionary process between people and plants that started at the beginning of the ARE occupation.