BACKGROUND: Microbial community dynamics during the anaerobic digestion of vinasse has been little studied. However, having knowledge about it is essential for early detection of reactor operational difficulties to apply preventive actions. This research studies the microbial community dynamics in the anaerobic digestion of vinasse, linking to experimental observations about product yields and organic matter degradation. RESULTS: Methane and sulfide yields decreased with increasing SO₄ ^2-/COD ratio, while the fraction of organic matter degraded by sulfate reducing bacteria increased from 4.5 ± 0.3% to 27.1 ± 0.6%. The archaeal community showed that acetoclastic Methanosaetaceae were little affected by the increase of the SO₄ ^2-/COD ratio, in contrast to the Methanomicrobiales and Methanobacteriales population, which decreased during the experiment. The total bacterial diversity was influenced mainly by substrate composition, showing that the increase of the SO₄ ^2-/COD ratio above 0.10 shifted the bacterial community to a lower richness. CONCLUSION: These results provide knowledge on the dynamics of the microbial communities, which can be useful to control the anaerobic digestion of sulfate-rich vinasses, showing that reactor stability equates to the higher ratios between total methanogens and total bacteria gene copy numbers, whereas operational difficulties can be associated to lower bacterial richness and higher community organization.