Abstract Soils are indispensable for the provision of several functions. Agricultural intensification and its focus on increasing primary productivity (PP) poses a threat to soil quality, due to increases in nutrient loads, greenhouse gas emissions and declining biodiversity. The EU Horizon 2020 Landmark project has developed multi‐criteria decision models to assess five soil functions: PP, nutrient cycling (NC), soil biodiversity and habitat provision (B‐HP), climate mitigation and water regulation, simultaneously in agricultural fields. Using these algorithms, we evaluated the supply of PP, NC and B‐HP of 31 grasslands and 21 croplands as low, medium or high. The multi‐criteria decision models showed that 38% of the farms had a medium to high supply of all three soil functions, whereas only one cropland had a high supply for all three. Forty‐eight per cent of the farms were characterized by a high supply of PP and NC. We observed a clear trade‐off between these two functions and B‐HP. Multivariate statistical analyses indicated that higher organic inputs combined with a lower mineral fertilization concur with higher biodiversity scores while maintaining a medium delivery of PP and NC. Additionally, we compared the outputs of the model predictions to independent variables that served as proxies for the soil functions and found: (a) croplands (but not grasslands) with high PP had a higher standardized yield than those with medium PP; (b) grasslands (but not croplands) with high NC had a significantly lower fungal to bacterial biomass ratio, suggesting faster decomposition channels; and (c) a positive though non‐significant trend between B‐HP score and rank according to soil invertebrate biodiversity. These comparisons suggest a successful upscaling of the models from field to farm level. Our study highlights the need for systematic collection of management‐related data for the assessment of soil functions. Multifunctionality can be achieved in agricultural soils; however, without specifically managing for it, biodiversity might come at a loss. Highlights We study how well soils can provide primary productivity, nutrient cycling and biodiversity. We study trade‐offs and synergies among soil functions, as well as the drivers of these relationships. Soil biodiversity is largely sacrificed for primary productivity and nutrient cycling Changes in pesticide and fertilizer management can increase soil multifunctionality.