Rice in southern South America is mainly associated with livestock production in rotation with pastures of three to four years in length, but there is interest in intensifying production by increasing the frequency of rice, introducing new crops, or shortening the pasture in the rotation. However, little is known about the impact of this perturbation on agroecosystems resilience. In 2012, a long-term experiment was established in the main rice-producing area of Uruguay to study the impact of the intensification of rotations on the sustainability of rice systems. After one cycle, soil microbial communities were studied in six different rotations using high-throughput sequencing to compare microbial community changes after agroecosystem disturbances caused by intensification. 3662 and 807 bacterial and fungal OTUs were detected. No major differences were found in the indicators of the diversity of microbial communities between rotations. Actinobacteria, Firmicutes, and Proteobacteria were the most common bacterial phyla, but only Proteobacteria differed between rotations. Most of the fungal OTUs were not identified, but Ascomycota, and to a lesser extent, Basidiomycota, and Mucoromycota were the most abundant classes. Only P and C:N varied between rotations after six years, and bacterial OTUs were weakly influenced by P, pH, Mg, and fungal OTUs by P. The results suggest that the bacterial / archaea communities were influenced by the frequency of rice in the rotation, and the fungal communities were more influenced by the previous crop. More studies are needed to associate fungal communities with environmental or rotational variables. Some bacterial taxa were associated with a particular rotation and were identified as biomarkers. No fungal indicator taxa were identified at the species level for any rotation. © 2023 Elsevier B.V.