The causes of late-Holocene centennial to millennial scale climatic variability and the impact that such variability had on tropical ecosystems are still poorly understood. Here, we present a high-resolution, multiproxy record from lowland eastern Mesoamerica, studied to reconstruct climate and vegetation history during the last 2,000 years, in particular to evaluate the response of tropical vegetation to the cooling event of the Little Ice Age (LIA). Our data provide evidence that the densest tropical forest cover and the deepest lake of the last two millennia were coeval with the LIA, with two deep lake phases that follow the Spörer and Maunder minima in solar activity. The high tropical pollen accumulation rates limit LIA's winter cooling to a maximum of 2 degrees C. Tropical vegetation expansion during the LIA is best explained by a reduction in the extent of the dry season as a consequence of increased meridional flow leading to higher winter precipitation. These results highlight the importance of seasonal responses to climatic variability, a factor that could be of relevance when evaluating the impact of recent climate change.