Abstract Madagascar comprises one of the Earth’s biologically richest, but also one of most endangered, terrestrial ecoregions. Although it is obvious that humans substantially altered its natural ecosystems during the past decades, the timing of arrival of humans on Madagascar as well as their environmental impact is not well resolved. In this context, this research aims to study and compare the influence of early human impact and climate change on rain forests and wildlife in northern Madagascar during the past Millennia. By using palaeoenvironmental reconstructions from lake sediment cores in a montane environment (Montagne d’Ambre), results indicate a major drought, starting approximately 1,100 years ago. This drought caused significant changes in lake levels and vegetation dynamics. Human impact, evidenced by fires, started a few decades later. Anthropogenic burning, limited to the low-altitude areas, was therefore not the driving force behind these early changes observed in the lake catchment areas. Although this does not dismiss the strong impacts humans had subsequently on these ecosystems, this work demonstrates that the late Holocene natural drought that intensified regionally about one thousand years ago, significantly impacted the ecosystems independently and prior to anthropogenic activities. At a regional scale, a review of demographic studies revealed a substantial number of inferred population bottlenecks in various wildlife species during the last millennia, likely resulting from this combination of both human-related impact and natural environmental changes (i.e., precipitation decline). This research highlights that the current state of ecosystems in northern Madagascar results from both human impact and natural climate changes. It also points to the importance of a multi-site and multi-proxy comparison for deciphering the nature and succession of past environmental changes.