Cocoa bean fermentation is carried out in different production areas following various methods. This study aimed to assess how the bacterial and fungal communities were affected by box, ground or jute fermentation methods, using high-throughput sequencing (HTS) of phylogenetic amplicons. Moreover, an evaluation of the preferable fermentation method was carried out based on the microbial dynamics observed. Box fermentation resulted in higher bacterial species diversity, while beans processed on the ground had a wider fungal community.Lactobacillus fermentumandPichia kudriavzeviiwere observed in all three fermentation methods studied. Moreover,Acetobacter tropicalisdominated box fermentation andPseudomonas fluorescensabounded in ground-fermented samples.Hanseniaspora opuntiaewas the most important yeast in jute and box, whileSaccharomyces cerevisiaeprevailed in the box and ground fermentation. PICRUST analysis was performed to identify potential interesting pathways. In conclusion, there were noticeable differences between the three different fermentation methods. Due to its limited microbial diversity and the presence of microorganisms that guarantee good fermentation, the box method was found to be preferable. Moreover, the present study allowed us to thoroughly explore the microbiota of differently treated cocoa beans and to better understand the technological processes useful to obtain a standardized end-product.