The aim of the present work was to evaluate the use of the kefir grains as a starter culture for new cocoa (Theobroma cacao L.) beverages. Fermentation was performed by inoculating kefir grains in cocoa pulp. Flasks containing kefir grains and different substrates were statically incubated at 10 and 25 °C for 48 and 72 h. The microbiota of Brazilian kefir grains and kefir cocoa beverages was characterized using molecular techniques. Denaturing gradient gel electrophoresis displayed communities included yeasts: Kluyveromyces marxianus, Saccharomyces cerevisiae, Kazachstania unispora, and bacteria: Lactobacillus kefiranofaciens subsp. kefirgranum, Lactobacillus kefiranofaciens subsp. kefiranofaciens, Lactobacillus plantarum, Lactobacillus fermentum, and a bacterium related to the genus Acetobacter. A microbial steady structure was detected in the analyzed kefir cocoa beverages and kefir grains. This robustness is determinant for future implementation of cocoa-based kefir beverages. The lactic, acetic, malic, propionic and citric acid contents increased during the 72 h of fermentation process in kefir beverages, reaching maximum value of ~ 5.55 g L− 1, ~ 1.0 g L− 1, ~ 0.3 g L− 1, ~ 1.0 g L− 1 and ~ 3.0 g L− 1 respectively. Oxalic, tartaric, butyric acids and glycerol were detected in similar concentrations. These compounds were found during the 48 and 72 h fermentation period at 10 and 25 °C in low concentration of ~ 1.4 g L− 1. Methanol also was detected in low concentration of ~ 0.8 g L− 1. The beverages fermented at 10 °C during 48 and 72 h produce lower amounts of ethanol ~ 4.5 g L− 1 (0.36% v/v). These beverages had the greater acceptance (92% and 100% of the panelist, respectively) based on taste, odor, and appearance of the beverages. The best acceptance may be due to low acidity/alcoholic concentration in the beverages. In this study it was possible to produce alcoholic kefir beverages (ethanol concentration of, ~ 45.0 g L− 1 (3.6% v/v)) with cocoa pulp fermentation for a period of 48 and 72 h at 25 °C. These beverages had acceptance by 80% of the panelist. This study is the first to report the alcoholic kefir beverage production from cocoa. Based on the chemical characteristics and acceptance in the sensory analysis, these results open up perspectives for this innovative application of kefir grains for developing cocoa pulp-based beverages.