Through a meta-analysis, Mupepele et al. (BMC Ecol Evol 21:1–193, 2021) assessed the effects of European agroforestry systems on biodiversity, estimated by species richness or species diversity. They showed that the effects of silvoarable and silvopastoral systems depend on the systems they are compared to and the taxa studied. Further, they found that only silvoarable systems increased species richness or diversity, compared to cropland. The authors conclude that agroforestry systems have weak effects on biodiversity and that landscape context or land-use history are probably more important than the practice of agroforestry in itself. However, we draw attention to important shortcomings in this meta-analysis, which downplay the potential of agroforestry for biodiversity conservation in agricultural landscapes. We hope that the meta-analysis by Mupepele et al. (BMC Ecol Evol 21:1–193, 2021), and our comments, will contribute to improving the quality of research on agroforestry systems and biodiversity conservation.