Background and aims <p>Microbes in the rhizosphere play a crucial role in regulating various agroecosystem functions that determine crop productivity. While management practices influence the structure and composition of these microbial communities, our understanding of this influence in farmers' fields remains limited at regional scale.</p> Methods <p>In this study, we conducted an on-farm study to investigate the rhizosphere microbiome of crops grown under conventional and organic management. We collected rhizosphere samples from 30 conventionally managed and 23 organically managed farms in the Midwest USA, and&#xa0;analyzed the associated bacterial and fungal communities for diversity, co-occurrence patterns, biomarkers, and functional traits.</p> Results <p>Our findings revealed significantly higher fungal richness under organic management. Both bacterial and fungal communities were strongly influenced by management practices, but only fungi were shaped by the&#xa0;host plant. Notable biomarker taxa included Burkholderiales and Cantharellales in organic fields, and Thermomicrobiales and Malasseziales in conventional fields. Microbial network connectivity and modularity were greater under organic management. Gaiellales and Tistrellales emerged as putative keystone taxa in organic systems, while Tistrellales and Rhizobiales were prominent in conventional systems. Rhizosphere soils under organic management contained fewer putative fungal pathogens and a higher abundance of bacteria involved in cellulolysis and hydrocarbon degradation.</p> Conclusions <p>Overall, this on-farm study integrates field data and spatial heterogeneity to highlight enhanced microbiome connectivity and reduced pathogen presence in the rhizosphere under organic agriculture. These results underscore the potential of adopting organic practices to enhance crop productivity and sustainability in agroecosystems.</p>