The effect of agricultural practices on soil bacterial communities is not constant and depends a lot on the climatic context, changes in the soil characteristics, land use, and agricultural strategy. Thus, knowledge about how different land use systems in the Cerrado influence the diversity and taxonomic structure of microbial communities under the same soil type remains limited. In this context, the objective of this work was to analyze and compare the bacterial communities of Cerrado soil under two different land use systems (cover crop and potato cultivation) and in a neighboring native Cerrado area. For this, we used high-throughput amplicon sequencing of 16S rRNA genes (metabarcoding) to characterize the bacterial community at different taxonomic levels in a native Cerrado area, in a potato crop area, and in an area with cover crops. Our data indicated significant impacts on soil physicochemical properties and enzymatic activity, which directly reflect the dynamics of bacterial communities. The three bacterial phyla with the highest relative abundance in the three areas were Proteobacteria, Actinobacteriota, and Acidobacteriota. At the taxonomic class level, small variations were observed among areas, while at the amplicon sequence variant (ASV) level, these variations were more pronounced. The alpha diversity indices showed that the bacterial communities among the areas are rich and diverse. Bray-Curtis and Jaccard distance-based PCoA demonstrated an overlap of bacterial communities present in the cover crop area with the native Cerrado area and separation from the potato cultivation area. The in silico prediction demonstrated that the native Cerrado area presented the highest values of functional diversity of the soil bacterial community compared to the others. Thus, our results provide a holistic view of how different land use systems in the Cerrado can influence the taxonomic and functional diversity of soil bacterial communities.