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• Deforestation-induced rainfall changes negatively impact soybean and maize yields in Brazil. • Soybean and maize yields could have been 6.6 % and 9.9 % higher per year if rainfall patterns hadn't been altered by deforestation. • Agricultural efficiency improvements insufficient to counteract rainfall-changes effects on yields. • Study underscores the vital role of forest preservation for agricultural resilience and food security. • Forests' critical role in regulating the water cycle highlighted in the face of climate change. Whereas the global demand for food, fiber and energy is increasing, the capacity of ecosystems services to sustain agricultural production is being compromised worldwide. Brazil is a global food supplier that has benefitted from agricultural intensification in the past decades. At the same time, expansion of cropland has led to deforestation that, in turn, is increasingly affecting rainfall patterns thereby influencing crop yields. This study examines how loss in forest cover has impacted agricultural yields through change in rainfall. To do so, we use modelled data on changes in rainfall patterns due to deforestation as input to a crop model. We assess yield changes within the soybean-maize double cropping system, the country's most relevant agricultural system, in five states within the Amazon and Cerrado biomes. Findings revealed that soybean and maize yields would have been respectively 6.6 % and 9.9 % higher per year in the last decade if rainfall patterns hadn't been altered by deforestation from 1982 onwards. Although agricultural efficiency improved between 2011 and 2020, it was insufficient to offset the negative effect of altered rainfall on yields. Our paper reveals the link between deforestation and crop yields, emphasizing the need to preserve forest cover for agricultural resilience and food security. It reinforces the critical role of forests in regulating the water cycle, particularly in the face of climate change-induced warmer and drier conditions that can impact agricultural production and other human activities. [ABSTRACT FROM AUTHOR]