Climate change has been modifying precipitation and temperature in many regions of the world, prompting changes in plant communities. It also affects soil microbial communities, indirectly influencing plant species distribution through plant-soil feedbacks. Here we report an experiment designed to test seed germination responses to global change, addressed through the interaction between increased temperature and soil microbial communities in a tree species in the Atlantic rainforest, a global biodiversity hotspot. Our objective was to test plant-soil feedbacks in an early colonizer tree species, Schizolobium parahyba, and their interaction with warming. We assessed the role of increased air temperature and soil microbiota in controlling seed germination as a function of distance to mother tree. Higher germination percentages were recorded with extracts of soil microbial communities from the edge of the canopy than with microbial extracts obtained closer to the trunk. These manipulations evidenced that soil microbiota influenced seed germination, being responsible for Janzen–Connell effects. Warming produced major changes in microbial composition but the effect on germination was unclear. Our results may help understand species distribution and coexistence in secondary patches of Atlantic rainforest under warmer conditions, and may contribute to the design of successful restoration programs.