Soil and soil-biodiversity protection are increasingly important issues in environmental science and policies, requiring the availability of high-quality empirical data on soil biodiversity. Here we present a publicly available data warehouse for the soil-biodiversity domain, Edaphobase 2.0, which provides a comprehensive toolset for storing and re-using international soil-biodiversity data sets, following the FAIR (Findable, Accessible, Interoperable, and Reusable) principles. A major strength is the possibility of annotating biodiversity data with exhaustive geographical, environmental and methodological metadata, allowing a wide range of applications and analyses. The system harmonises and integrates heterogeneous data from diverse sources into standardised formats, which can be searched together using numerous filter possibilities, and offers data exploration and analysis tools. Edaphobase features a strict data transparency policy, comprehensive quality control, and DOIs can be provided for individual data sets. The database currently contains >450,000 data records from >35,0000 sites and is accessed nearly 14,000 times/year. The data curated by Edaphobase 2.0 can greatly aid researchers, conservationists and decision makers in understanding and protecting soil biodiversity.