Cacao demand is continuously increasing, and variations in cacao prices have been associated with the aroma of fermented cacao beans. However, the role of microorganisms in the formation of volatile-aroma compounds during fermentation remains unclear. Microbial diversity in Nacional × Trinitario cacao was characterized during spontaneous fermentation by using culture-based methods and next-generation sequencing (NGS) of DNA amplicons. Cacao beans that were spontaneously fermented for 0, 24, 48, 72 and 96 h were UV-sterilized prior to the inoculation of the microbial isolates obtained by the culture-based methods. The volatile formation in inoculated cacao beans was evaluated by GC-MS. The species isolated during fermentation included yeast, such as and lactic acid bacteria (LAB), such as and acetic acid bacteria (AAB), such as , and , as well as other species, such as and . Additionally, NGS revealed an abundance of environmental microorganisms, including spp., spp., spp., spp., spp. and spp., among others. During the lab-scale fermentation, the inoculation of mostly yielded alcohols, while LAB and AAB produced volatiles associated with floral, almond and fruity notes throughout the fermentation, but AAB also produced acetic acid with a sour aroma. Similarly, the inoculation of and spp. in 96 h fermented cacao beans yielded esters with floral aromas. This is the first report describing the role of microorganisms in volatile formation during fine-flavor cacao fermentation.