•Sequencing was crucial to identify the bacterial succession during fermentation.•Food safety is a factor important in the microbial fermentations of coffee.•Fermentation at 38 °C promotes more shifts in the bacterial composition.•High temperature and time of fermentation favors Lactobacillus sp.•Relative abundance of Lactobacillus is directly correlated with sensory scores. The diversity and activity of the indigenous microorganisms in coffee are essential for obtaining safe and good-quality coffee. The use of fermentation under carbonic maceration in coffee fruits showed a positive correlation between the bacterial community and sensory score. Thus, the objective of this study was to evaluate the bacterial diversity in coffee cherries during fermentation under carbonic maceration and their correlations with coffee-quality. Next-generation sequencing and Specialty Coffee Association protocol were used in this study. Predominance of Leuconostoc sp. and Lactobacillus sp. during fermentation was observed. Leuconostoc sp. had higher relative abundance in the initial phase of fermentation and at 18 and 28 °C than Lactobacillus sp. Furthermore, the greatest microbial diversity occurred at 38 °C and after 72 h. At this temperature, the relative abundance of Lactobacillus correlated positively with sensorial score. Thus, an increase in temperature and fermentation time favors Lactobacillus spp and coffee sensory quality.