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Natural regeneration provides multiple benefits to nature and human societies, and can play a major role in global and national restoration targets. However, these benefits are context specific and impacted by both biophysical and socioeconomic heterogeneity across landscapes. Here, we investigate the benefits of natural regeneration for climate change mitigation, sediment retention and biodiversity conservation in a spatially explicit way at very high resolution for a region within the global biodiversity hotspot of the Atlantic Forest. We classified current land-use cover in the region and simulated a natural regeneration scenario in abandoned pasturelands, areas where potential conflicts with agricultural production would be minimized and where some early stage regeneration is already occurring. We then modeled changes in biophysical functions for climate change mitigation and sediment retention, and performed an economic valuation of both ecosystem services. We also modeled how land-use changes affect habitat availability for species. We found that natural regeneration can provide significant ecological and social benefits. Economic values of climate change mitigation and sediment retention alone could completely compensate for the opportunity costs of agricultural production over 20 yr. Habitat availability is improved for three species with different dispersal abilities, although by different magnitudes. Improving the understanding of how costs and benefits of natural regeneration are distributed can be useful to design incentive structures that bring farmers’ decision making more in line with societal benefits. This alignment is crucial for natural regeneration to fulfill its potential as a large-scale solution for pressing local and global environmental challenges.