Microbial communities play a key role in the ocean, acting as primary producers, nutrient recyclers, and energy providers. The São Paulo Plateau is a region located on the southeastern coast of Brazil, with economic importance due to its oil and gas reservoirs. The main objective of this study was to evaluate the diversity and composition of microbial communities and the possible predicted functions. Sediment samples were collected from three strata (superficial, intermediate, and deep) in three stations (SP1, SP2, and SP3) located in the southern region of the Plateau of São Paulo using the HOV Shinkai 6500 in 2013. The 16S rRNA gene was sequenced using primers universals (515F and 926R) by the Illumina Miseq platform. Taxonomic data showed that the SP1 station had the highest relative abundance of the class Nitrososphaeria in the superficial (17%) and deep (21%) strata. The samples from stations SP2 and SP3 showed very similar taxonomic compositions. The SP2 station showed a predominance of Gammaproteobacteria, representing 15%, 38%, and 30% in the superficial, intermediate, and deep strata, respectively. Station SP3 also showed the dominance of Gammaproteobacteria in the superficial and inferior strata (92% and 90%, respectively). With metabolic prediction, it was observed that chemoheterotrophy and fermentation were predicted in almost all samples. The core microbiome analysis comprised only two ASVs. Our study contributes to a better understanding of microbial communities in an economically important and ecologically little-explored region. This is the second microbiological survey in plateau sediments and the first focused on the southern region.