Deforestation threatens global soil biodiversity and ecosystem services. A global dataset of 696 paired-site observations shows that converting native forests to plantations, grasslands, and croplands reduces soil biodiversity and ecosystem functions, including carbon storage, nutrient cycling, and organic matter decomposition. These conversions lead to more homogeneous fungal communities dominated by pathogens and reduced symbiotic fungi. Soil microbial diversity and functions are most affected when forests are converted to croplands, especially in warmer and wetter ecosystems. Soil pH and total phosphorus are key drivers of microbial community responses to deforestation. The study highlights the importance of avoiding soil degradation caused by deforestation to conserve soil biodiversity and ecosystem services. Native forests are critical for maintaining soil biodiversity and ecosystem services, but deforestation has led to dramatic changes in forest cover. Conversion of native forests to managed ecosystems results in soils with reduced capacity to support plant pathogen regulation, plant-soil symbiosis, and nutrient cycling. The loss of native forests to managed ecosystems poses a major threat to soil biodiversity and ecosystem services. The study provides the most complete global database to investigate the impacts of deforestation on soil conservation. The results show that deforestation leads to critical reductions in soil ecosystem services, including soil carbon storage and nutrient cycling. The study also reveals that deforestation promotes soil fungal plant pathogens and reduces fungal symbionts, negatively affecting ecosystem health and productivity. The findings emphasize the need for conservation strategies to protect soil biodiversity and function. The study used a mixed-effects meta-regression analysis to examine the relationships between soil properties, microbial diversity, and ecosystem functions. The results indicate that changes in soil biodiversity and functions are influenced by soil pH, total phosphorus, and climate factors. The study highlights the importance of considering abiotic factors in understanding the impacts of deforestation on soil ecosystems. The findings suggest that deforestation has a greater negative effect on fungal diversity in warmer and wetter ecosystems, but supports the growth of fast-turnover bacteria. The study also shows that deforestation reduces the ability of key fungal taxa to secrete extracellular enzymes to decompose organic matter or acquire nutrients to promote plant growth. The results indicate that changes in microbial diversity and the loss of key taxa after native forest conversion negatively affect organic matter decomposition, leading to more abiotic-driven soil with reduced functionality. The study provides a comprehensive understanding of the impacts of deforestation on soil biodiversity and ecosystem services, emphasizing the need for conservation strategies to protect soil biodiversity and function.Deforestation threatens global soil biodiversity and ecosystem services. A global dataset of 696 paired-site observations shows that converting native forests to plantations, grasslands, and croplands reduces soil biodiversity and ecosystem functions, including carbon storage, nutrient cycling, and organic matter decomposition. These conversions lead to more homogeneous fungal communities dominated by pathogens and reduced symbiotic fungi. Soil microbial diversity and functions are most affected when forests are converted to croplands, especially in warmer and wetter ecosystems. Soil pH and total phosphorus are key drivers of microbial community responses to deforestation. The study highlights the importance of avoiding soil degradation caused by deforestation to conserve soil biodiversity and ecosystem services. Native forests are critical for maintaining soil biodiversity and ecosystem services, but deforestation has led to dramatic changes in forest cover. Conversion of native forests to managed ecosystems results in soils with reduced capacity to support plant pathogen regulation, plant-soil symbiosis, and nutrient cycling. The loss of native forests to managed ecosystems poses a major threat to soil biodiversity and ecosystem services. The study provides the most complete global database to investigate the impacts of deforestation on soil conservation. The results show that deforestation leads to critical reductions in soil ecosystem services, including soil carbon storage and nutrient cycling. The study also reveals that deforestation promotes soil fungal plant pathogens and reduces fungal symbionts, negatively affecting ecosystem health and productivity. The findings emphasize the need for conservation strategies to protect soil biodiversity and function. The study used a mixed-effects meta-regression analysis to examine the relationships between soil properties, microbial diversity, and ecosystem functions. The results indicate that changes in soil biodiversity and functions are influenced by soil pH, total phosphorus, and climate factors. The study highlights the importance of considering abiotic factors in understanding the impacts of deforestation on soil ecosystems. The findings suggest that deforestation has a greater negative effect on fungal diversity in warmer and wetter ecosystems, but supports the growth of fast-turnover bacteria. The study also shows that deforestation reduces the ability of key fungal taxa to secrete extracellular enzymes to decompose organic matter or acquire nutrients to promote plant growth. The results indicate that changes in microbial diversity and the loss of key taxa after native forest conversion negatively affect organic matter decomposition, leading to more abiotic-driven soil with reduced functionality. The study provides a comprehensive understanding of the impacts of deforestation on soil biodiversity and ecosystem services, emphasizing the need for conservation strategies to protect soil biodiversity and function.