This study aimed to determine the impact of different agroecological practices on the composition and diversity of edaphic bacterial and fungal communities. We designed two experimental agroecological vegetable cropping systems and analyzed their effects on soil microbial communities by pyrosequencing the 16S and 18S ribosomal RNA genes. Our results highlighted modifications to the Operational Taxonomic Units in both experimental systems compared with bare soil, particularly for the phyla Actinobacteria, Ascomycota, Bacteroidetes, and Mucoromycota. Multidimensional scaling plots based on beta diversity showed a clear distinction between the two experimental systems for fungi, whereas differences were observed between bare soil and the two experimental systems for bacteria. Overall, the agroecological systems enhanced soil microbial diversity. We showed a distinction between the two experimental systems and bare soil, correlated with the high total N and total P contents in the agroecological systems. Both experimental systems promoted soil enrichment with certain essential minerals. The agroecological systems had a positive impact on soil microbial communities, particularly by promoting the development of beneficial soil bacteria like Actinobacteria. In the two experimental systems, changes in the quality and quantity of organic matter (i.e. mulch, vermicompost, plant diversity) could have modified the abundance and diversity of microbial communities.