Unsustainable soil management, climate change, and land degradation jeopardize soil biodiversity and soil-mediated ecosystem functions. Although the transition from conventional to organic agriculture has been proposed as a potential solution to alleviate these pressures, there is limited evidence of its effectiveness in enhancing belowground biodiversity across different biogeographical regions, climates, and land degradation levels. In this study, we holistically assessed the status of soil biodiversity, from microorganisms to meso- and macrofauna, in agroecosystems distributed across four continents. We identified the primary environmental community composition drivers and assessed the effects of the transition from conventional to organic management (no chemical inputs) on soil ecology. Our findings highlight the mean temperature and precipitation of the warmest and coldest quarters of the year, aridity, pH, and soil texture as the primary drivers of the different soil biodiversity components. Overall, organic farming has a significant but small impact on soil biodiversity compared to the other community drivers. On top of that, the results demonstrate the importance of a regional-specific context for a future generalized transition towards organic soil management. Specifically, under the most arid conditions in our study, organic management showed potential to buffer biodiversity loss in highly degraded soils, with a significant increase in diversity for prokaryotes and protists compared to conventionally managed soils. Therefore, the combination of a global and, simultaneously, regional-specific approach supports the hypothesis that a shift towards organic agriculture would maximize its beneficial impact on belowground diversity in highly degraded soils under arid conditions over the coming years, being a crucial tool to increase resilience and adaptation to global change for agriculture.