Species migrations in response to climate change have already been observed in many taxonomic groups worldwide. However, it remains uncertain if species will be able to keep pace with future climate change. Keeping pace will be especially challenging for tropical lowland rainforests due to their high velocities of climate change combined with high rates of deforestation, which may eliminate potential climate analogs and/or increase the effective distances between analogs by blocking species movements. Here, we calculate the distances between current and future climate analogs under various climate change and deforestation scenarios. Under even the most sanguine of climate change models (IPSL_CM4, A1b emissions scenario), we find that the median distance between areas in the Amazon rainforest and their closest future (2050) climate analog as predicted based on just temperature changes alone is nearly 300 km. If we include precipitation, the median distance increases by over 50% to >475 km. Since deforestation is generally concentrated in the hottest and driest portions of the Amazon, we predict that the habitat loss will have little direct impact on distances between climate analogs. If, however, deforested areas also act as a barrier to species movements, nearly 30% or 55% of the Amazon will effectively have no climate analogs anywhere in tropical South America under projections of reduced or Business-As-Usual deforestation, respectively. These ‘disappearing climates’ will be concentrated primarily in the southeastern Amazon. Consequently, we predict that several Amazonian ecoregions will have no areas with future climate analogs, greatly increasing the vulnerability of any populations or species specialized on these conditions. These results highlight the importance of including multiple climatic factors and human land-use in predicting the effects of climate change, as well as the daunting challenges that Amazonian diversity faces in the near future.