Biological nitrogen fixation contributes greatly to the sustainability of agroecosystems. However, more information is needed about the impact that agricultural intensification, a frequent practice nowadays, would have on diazotrophic communities associated with plants. This work addresses the influence of intensifying rice cropping systems on the abundance, diversity, and structure of diazotrophic communities associated with rice roots (rhizospheric and endophytic bacteria) from a field experiment. Three different rice rotation systems (rice-pasture, rice-soybean, and continuous rice) at two crop growth stages (TBF:tillering before flooding and FF:flowering-flooded) were studied. The results showed that the rhizospheric soils had the greater nifH gene abundance, and the abundance and diversity of rhizospheric and endophytic diazotrophic communities significantly increased at the FF stage. Conversely, nifH abundance in bulk soils remained unaltered. Phylogenetically and metabolically diverse diazotrophic communities were found to be associated with rice roots from the different crop stages and rotations. © The Author(s) under exclusive licence to Society for Environmental Sustainability 2023