Cocoa fermentation is the first step in the post-harvest processing chain of cocoa and is important for the removal of the cocoa pulp surrounding the beans and the development of flavor and color precursors. In the present study, metagenomic and metatranscriptomic sequencing were applied to Costa Rican cocoa fermentation processes to unravel the microbial diversity and assess the function and transcription of their genes, thereby increasing the knowledge of this spontaneous fermentation process. Among 97 genera found in these fermentation processes, the major ones were , , , and The most prominent species were , , and among the LAB, and among the AAB, and and among the yeasts. Consumption of glucose, fructose, and citric acid, and the production of ethanol, lactic acid, acetic acid, and mannitol were linked to the major species through metagenomic binning and the application of metatranscriptomic sequencing. By using this approach, it was also found that consumed mannitol and oxidized lactic acid, that degraded oxalate, and that species such as sp., spp., and could contribute to pectin degradation. The data generated and results presented in this study could enhance the ability to select and develop appropriate starter cultures to steer the cocoa fermentation process toward a desired course.