This is the dataset used for the analyses in the paper "Planting food forests can increase soil biodiversity in agricultural landscapes of Northwest Europe" published in npj Biodiversity (doi: 10.1038/s44185-026-00125-w). It contains all necessary files to conduct the analyses on the total biomass or number of individuals, alpha-diversity, community composition and beta-diversity of bacteria, non-arbuscular mycorrhizal fungi, arbuscular mycorrhizal fungi, protists, nematodes, springtails, mites, isopods, millipedes, centipedes, harvestmen, carabids and earthworms presented in the publication. The R-scripts used to process and analyse the data (along with some information on the files) can be found at https://github.com/MLieke/soil-biodiversity-food-forests (as compared to v1 of this dataset, the only change is an update of two species identifications in the Harvestmen.csv file)