Since cocoa seed fermentation is a spontaneous and uncontrolled process, it is mediated by a complex microbial consortium that significantly affects the quality of the final product. Given that Hanseniaspora spp. has been identified as a dominant genus during the fermentation process and that efficient microorganisms are required for use in starter cultures, this study aimed to analyze the genomes of Hanseniaspora spp. obtained from metagenomic shotgun sequencing of cocoa bean fermentation samples from the Ilhéus/BA region. The genomes of Hanseniaspora spp. were assembled using SPAdes, and gene ontologies (GO) were determined using OmicsBox, EggNOG, and REVIGO. The main biological activities identified in the genes encoded by Hanseniaspora spp. revealed mechanisms associated with biogenesis, as well as the metabolism of carbohydrates, aromatic compounds, glycoproteins, and organic acids, among others. These metabolic activities directly influence the production of volatile organic compounds, which contribute to the development of a diverse range of aromatic flavor molecules. The functional annotation performed indicates that Hanseniaspora spp. possesses a highly compatible metabolic profile suited for the fermentation process, suggesting its potential use as a starter inoculum.