Soil invertebrate communities represent a significant fraction of global biodiversity and play crucial roles in ecosystems. A number of human activities threaten soil communities, in particular intensive agricultural practices such as pesticide use. However, there is currently no quantitative synthesis of the impacts of pesticides on soil fauna communities. Here, using a meta-analysis of 54 studies and 294 observations, we quantify pesticide effects on the abundance, biomass, richness and diversity of natural soil fauna communities across a wide range of environmental contexts. We also identify scenarios with the most detrimental effects on soil fauna communities by analysing the effects of different pesticides (herbicides, fungicides, insecticides, broad-spectrum substances and multiple substances), different application rates and temporal extents (short- or long-term), as well as the response of different functional groups of soil animals (body size categories, presence of exoskeleton). Pesticides overall decreased the abundance and diversity of soil fauna communities across studies (Grand mean effect size (Hedge's g) = −0.30 +/− 0.16) and had stronger effects on soil fauna diversity than abundance. The most detrimental scenarios involved multiple substances, broad-spectrum substances and insecticides, which significantly decreased soil fauna diversity even at recommended rates. We found no evidence that pesticide effects dampen over time, as short-term and long-term studies exhibited similar mean effect sizes. Policy implications: Our study highlights that pesticide use has significant detrimental non-target effects on soil biodiversity, eroding a substantial part of global biodiversity and threatening ecosystem health. This provides crucial evidence supporting recent policies, such as the European Green Deal, that aim to reduce pesticide use in agriculture to conserve biodiversity. The detrimental effects of multiple substances revealed here are particularly concerning because realistic pesticide use often combines several substances targeting different pests and diseases over the crop season. We suggest that future guidelines for pesticide registration, restrictions and banning should rely on data able to fully capture the long-term consequences of multiple substances for multiple non-target species in realistic conditions.