16S rRNA gene sequencing dataset describing the diversity and structure of soil bacterial communities across four pesticide-free agroecological cropping systems of arable crops from the CA-SYS experiment between 2018 and 2021

A dataset describing soil bacterial community diversity and structure was generated from the CA-SYS experimental platform (INRAE, France), a long-term research facility designed to evaluate agroecological practices under contrasting soil management without pesticide use. Soil samples were collected from 42 experimental plots (4 subplots per plot) across four cropping systems, including no-till and tilled systems with or without nitrogen inputs, over four sampling years (2018–2021). It comprises 640 samples for which sequencing data were obtained, and 595 samples after quality control, representing 10,633 operational taxonomic units (OTUs) derived from 16S rRNA gene amplicon sequencing. Available data include raw sequencing reads deposited in a public repository, an OTU count table with taxonomic annotation, a sample metadata table describing experimental design and management variables, and phyloseq objects in R format. Reproducible analysis outputs are also provided as HTML documents describing data structure, quality control procedures, and diversity metrics. These data provide a structured resource for exploring soil bacterial community composition across contrasting pesticide-free agroecological cropping systems in arable crops. The availability of curated data objects and associated metadata facilitates reuse for methodological developments, benchmarking of bioinformatics workflows, and comparative analyses with other soil microbiome datasets.