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Summary Efficient resource use is a key factor for sustainable production and a necessity for meeting future global food demands. However, the factors that control resource use efficiency in agro‐ecosystems are only partly understood. We investigated the influence of soil biota on nutrient leaching, nutrient‐use efficiency and plant performance in outdoor, open‐top lysimeters comprising a volume of 230 L. The lysimeters were filled with sterilized soil in two horizons and inoculated with a reduced soil‐life inoculum (soil biota ≤11 μm, microbially dominated) and an enriched soil‐life inoculum [soil organisms ≤2 mm, also containing arbuscular mycorrhizal fungi ( AMF )]. A crop rotation was planted, and nutrient leaching losses, plant biomass and nutrient contents were assessed over a period of almost 2 years. In the first year of the experiment, enriched soil life increased crop yield (+22%), N uptake (+29%) and P uptake (+110%) of maize and strongly reduced leaching losses of N (−51%, corresponding to a reduction of 76 kg N ha −1 ). In the second year, wheat biomass (+17%) and P contents (+80%) were significantly increased by enriched soil life, but the differences were lower than in the first year. Enriched soil life also increased P mobilization from soil (+112%) and significantly reduced relative P leaching losses (−25%), defined as g P leached per kg P plant uptake, as well as relative N leaching losses (−36%), defined as kg N leached per kg N plant uptake, demonstrating that nutrient‐use efficiency was increased in the enriched soil‐life treatment. Synthesis and applications . Soil biota are a key factor determining resource efficiency in agriculture. The results suggest that applying farming practices, which favour a rich and abundant soil life (e.g. reduced tillage, organic farming, crop rotation), can reduce environmental impacts, enhance crop yield and result in a more sustainable agricultural system. However, this needs to be confirmed in field situations. Enhanced nutrient‐use efficiency obtained through farming practices which exert positive effects on soil biota could result in reduced amounts of fertilisers needed for agricultural production and reduced nutrient losses to the environment, providing benefits of such practices beyond positive effects on biodiversity.