Deforestation poses a significant threat to global biodiversity and ecosystem services. A global dataset of 696 paired-site observations was analyzed to investigate the impacts of converting native forests to plantations, grasslands, and croplands on soil properties, biodiversity, and functions. The study found that deforestation led to higher bacterial diversity and more homogeneous fungal communities dominated by pathogens, with lower abundance of symbionts. These changes resulted in significant reductions in carbon storage, nutrient cycling, and soil functional rates related to organic matter decomposition. Soil microbial community responses, including bacterial and fungal diversity and fungal guilds, were primarily regulated by changes in soil pH and total phosphorus. The vulnerability of soil fungal diversity and functioning in warmer and wetter native forests was particularly pronounced. The study highlights the critical importance of avoiding soil degradation caused by deforestation to conserve soils and their associated ecosystem services for future generations.Deforestation poses a significant threat to global biodiversity and ecosystem services. A global dataset of 696 paired-site observations was analyzed to investigate the impacts of converting native forests to plantations, grasslands, and croplands on soil properties, biodiversity, and functions. The study found that deforestation led to higher bacterial diversity and more homogeneous fungal communities dominated by pathogens, with lower abundance of symbionts. These changes resulted in significant reductions in carbon storage, nutrient cycling, and soil functional rates related to organic matter decomposition. Soil microbial community responses, including bacterial and fungal diversity and fungal guilds, were primarily regulated by changes in soil pH and total phosphorus. The vulnerability of soil fungal diversity and functioning in warmer and wetter native forests was particularly pronounced. The study highlights the critical importance of avoiding soil degradation caused by deforestation to conserve soils and their associated ecosystem services for future generations.