Since soil biodiversity sustains above-ground life, the European Union (EU) has recently announced its new Soil Strategy to better protect soil ecosystems as part of the Biodiversity Strategy for 2030. Also, the EU’s Farm to Fork Strategy and the Zero Pollution Action Plan aims for soil protection. However, the status of soil biodiversity protection has not been comprehensively assessed. Therefore, we explored regulatory, incentive-based, and knowledge-based instruments and strategic policy documents at the EU and national levels to determine whether they adequately protect soil biodiversity. Our review of 507 literature references concluded that only eight EU member states explicitly address threats to soil biodiversity in 14 regulatory instruments while 13 countries mainly focus on implicit threats to soil biodiversity, whereas six countries do not consider soil biodiversity. At the EU level, current directives and regulations only tackle individual threats to soil biodiversity. An EU-wide, legally binding protection could ensure a standardized minimum level of soil biodiversity protection while preventing surging costs of not acting. The EU Soil Health Law foreseen for 2023 could couple land management practices beneficial for soil biodiversity with incentive-based instruments. Simultaneously, models should be designed to predict soil biodiversity, considering soil biodiversity’s spatial and temporal heterogeneity.