Microorganisms play a key role in nutrient cycling in agriculture and can contribute to improve soil quality and enhance crop production. Thus, there is a need to identify the most suitable management practices which foster increases in soil microbial biomass and diversity. A meta-analysis was performed to assess changes in microbial abundance in agricultural soils affected by: (i) management practices (tillage, fertilization and crop diversification); and (ii) environmental factors, including climate characteristics and soil properties. The scope of the meta-analysis was to evaluate whether microbial abundances are affected or not by organic fertilization or no fertilization, crop diversification (intercropping and crop rotations) and conservation tillage (reduced tillage/no-tillage) as an alternative to intensive conventional monocultures in agriculture. Only papers showing data on phospholipid fatty acids (PLFAs), providing indicators about soil microbial (total PLFA), fungal and bacterial biomass reached a critical mass to perform the meta-analysis. Therefore, soil microbial diversity could not be analyzed considering different management practices. Results showed that intercropping and crop rotations only significantly increased the abundance of fungi, with the corresponding increase in the fungal-to-bacterial ratio. Organic fertilization contributed to significant increases in bacterial and fungal abundance and total PLFA compared to mineral fertilization. Contrarily, the lack of fertilization negatively affected total PLFA, with no significant effect on bacterial and fungal abundances. Reduced tillage significantly increased total PLFA, fungal and bacterial abundances compared to conventional tillage, while no tillage had only a positive effect on fungi. Thus, as a general pattern, the adoption of sustainable management practices, mostly organic fertilization and reduced tillage, has overall positive effects on soil total microbial, fungal and bacterial abundance. These variables were not related to soil physicochemical properties and climatic factors, suggesting a positive global effect of sustainable management practices on soil microbial abundances. Thus, this study shows new insights by a meta-analysis of global studies about the effect of sustainable management practices on soil microbial abundances, needed for land-managers, policy-makers and farmers to select sustainable cropping systems that enhance microbial abundance.