The department of Arauca, Colombia, is recognized for the sensory quality of its cocoa, influenced by agronomic practices and the fermentation process. The latter depends on the activity of microorganisms, mainly bacteria, which generate key metabolites that shape the sensory profile of chocolate. Various studies have identified variations in the richness, evenness, and dominance of bacterial communities involved in this process; however, these studies have been conducted under uncontrolled conditions. This study characterized the bacterial communities in the fermentation of cocoa beans from nine agroclimatic zones in Arauca. Fermentations were carried out under homogeneous conditions, with sampling every 12 hours up to 96 hours. DNA was extracted from the samples, and the V4 region of the 16S rRNA gene was sequenced. Bacteria from the families Enterobacteriaceae, Lactobacillaceae, and Acetobacteraceae were identified, revealing a marked microbial succession. Enterobacter predominated between 0-12 h; Weissella, Limosilactobacillus, and Leuconostoc between 12-72 h; and Acetobacter after 72 h. Fermentation time was the primary factor determining bacterial composition, surpassing the influence of agroclimatic zones. However, clustering analysis revealed two distinct groups: one consisting of zones 2, 3, 5, and 8, and another including zones 1, 4, 6, and 9, indicating a significant geographical influence. These findings provide new insights into the microbial dynamics of cocoa fermentation in Arauca and its impact on the sensory profile of chocolate, with the potential to optimize fermentation practices and enhance the final product quality.