This data set contains a data-mining performed to assess the impact of crop diversification, tillage and fertilizer type on soil microbial, fungal and bacterial abundance under arable crops worldwide by a further meta-analysis of the data. These data correspond to the open-access article " The impact of crop diversification, tillage and fertilization type on soil total microbial, fungal and bacterial abundance: A worldwide meta-analysis of agricultural sites " published in Agriculture Ecosystems and Environment. (doi:10.1016/j.agee.2022.107867), funded by the European Commission Horizon 2020 project SoildiverAgro [grant agreement 817819].