Transgenic Bt-crops have been genetically modified by inserting a Bacillus thuriengensis gene so the plant expresses a Cry toxin aimed for insect crop pests. Non-target soil invertebrates are particularly recognized for their contribution to plant nutrient availability and turnover of organic matter and it is therefore relevant to protect these invertebrate taxa. A number of studies have compared the population abundance and biomass of soil invertebrates in agricultural fields planted with genetically modified Bt crops and their conventional counterparts. Here, were review and analyze a selection of studies on Protista, nematodes, Collembola, mites, enchytraeids, and earthworms systematically to empower the evidence for asking the question whether population abundances and biomasses of soil invertebrates are changed by Bt crops compared to conventional crops. 6110 titles were captured, of which 38 studies passed our inclusion criteria, and a final number of 22 publications were subject to data extraction. A database with 2046 records was compiled covering 36 locations and the Bt types Cry1Ab, Cry1Ac, Cry3Bb1 and Cry3Aa. Comparative effect sizes in terms of Hedges’ g were calculated irrespectively of statistical significance of effects of the source studies. Cry effects on populations were compared across the studies in a meta-analysis employing a hierarchical Bayesian approach of weighted data according to the level of replication. The temporal development of effect sizes was modelled, thereby taking into account the variable duration of the field experiments. There was considerable variation among soil invertebrate orders, but the sample size was insufficient and the sample heterogeneity too large to draw any credible conclusions on the effect of Cry at the order level. However, across orders there was no significant effect of Cry on soil invertebrates.