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CONTEXT: In the European Union (EU-27) and UK, animal farming generated annually more than 1.4 billion tonnes of manure during the period 2016–2019. Of this, more than 90% is directly re-applied to soils as organic fertiliser. Manure promotes plant growth, provides nutritious food to soil organisms, adds genetic and functional diversity to soils and improves the chemical and physical soil properties. However, it can also cause pollution by introducing toxic elements (i.e., heavy metals, antibiotics, pathogens) and contribute to nutrient losses. Soil organisms play an essential role in manure transformation into the soil and the degradation of any potential toxic constitutes; however, manure management practices often neglect soil biodiversity. OBJECTIVE: In this review, we explored the impact of manure from farmed animals on soil biodiversity by considering factors that determine the effects of manure and vice versa. By evaluating manure's potential to enhance soil biodiversity, but also its environmental risks, we assessed current and future EU policy and legislations with the ultimate aim of providing recommendations that can enable a more sustainable management of farm manures. METHODS: This review explored the relationship between manure and soil biodiversity by considering 407 published papers and relevant legislative provisions. In addition, we evaluated whether benefits and risks on soil biodiversity are considered in manure management. Thereafter, we analysed the current legislation in the European Union relevant to manure, an important driver for its treatment, application and storage. RESULTS AND CONCLUSIONS: This review found that coupling manure management with soil biodiversity can mitigate present and future environmental risks. Our analyses showed that manure quality is more important to soil biodiversity than manure quantity and therefore, agricultural practices that protect and promote soil biodiversity with the application of appropriate, high-quality manure or biostimulant preparations based on manure, could accelerate the move towards more sustainable food production systems. Soil biodiversity needs to be appropriately factored in when assessing manure amendments to provide better guidelines on the use of manure and to reduce costs and environmental risks. However, radical changes in current philosophies and practices are needed so that soil biodiversity can be enhanced by manure management. SIGNIFICANCE: Manure quality in the EU requires greater attention, calling for more targeted policies. Our proposed approach could be applied by European Union Member States to include soil protection measures in national legislation, and at the EU level, can enable the implementation of strategic goals. Financiado para publicación en acceso aberto: Universidade de Vigo/CISUG