Environmental perturbations such as agricultural intensification may alter soil biodiversity in a manner that affects ecosystem functioning, but links are not well quantified. With this review we ask: (1) “How does agricultural intensification affect soil biodiversity?” and (2) “How do such changes in soil biodiversity affect ecosystem function?” We used meta-analysis to quantify responses across studies. Our results indicate that agricultural intensification can significantly alter soil biodiversity, with negative impacts of synthetic N fertilization on arbuscular mycorrhizal fungal (AMF) and faunal diversity, and positive effects on fungal- and microbial functional diversity. Bacterial diversity increased with low synthetic N input rates (< 150 kg N ha − 1 year − 1 ), with organic N inputs, and when application duration was > 5 years, suggesting that agricultural management practices that promote soil organic matter (SOM) accumulation and retention enhance bacterial biodiversity. Tillage negatively impacted soil faunal and bacterial diversity, but did not affect AMF, fungal or functional diversity, and organic farming relative to conventional farming did not affect soil biodiversity. Biodiversity manipulation studies indicate that changes in soil biodiversity affect ecosystem process rates, although manipulated biodiversity levels tend to exaggerate biodiversity losses and possibly overestimate consequences for ecosystem functioning relative to measured biodiversity losses from environmental perturbations. There is a need for more studies that evaluate how losses in soil biodiversity following environmental perturbations directly affect ecosystem functioning. Advances in analytical techniques to identify soil organisms and an increase in soil biodiversity manipulation experiments should help solidify links between environmental changes, soil biodiversity and ecosystem functioning.