Cherry stillage is a high strength organic wastewater arising from the manufacture of alcoholic products by distillation of fermented cherries. It is made up of biorefractory polyphenols in addition to readily biodegradable organic matter. An anaerobic sequencing batch reactor (AnSBR) was used to treat cherry stillage at influent COD ranging from 5 to 50 g/L. Different cycle times were selected to test biomass organic loading rates (OLRB), from 0.3 to 1.2 g COD/g VSS(.)d. COD and TOC efficiency removals higher than 80% were achieved at influent COD up to 28.5 g/L but minimum OLRB tested. However, as a result of the temporary inhibition of acetogens and methanogens, volatile fatty acids (VFA) noticeably accumulated and methane production came to a transient standstill when operating at influent COD higher than 10 g/L. At these conditions, the AnSBR showed signs of instability and could not operate efficiently at OLRB higher than 0.3 g COD/g VSS(.)d. A feasible explanation for this inhibition is the presence of toxic polyphenols in cherry stillage. Thus, an ozonation step prior to the AnSBR was observed to be useful, since more than 75% of polyphenols could be removed by ozone. The integrated process was shown to be a suitable treatment technology as the following advantages compared to the single AnSBR treatment were observed: greater polyphenols and color removals, higher COD and TOC removal rates thus enabling the process to effectively operate at higher OLR, higher degree of biomethanation, and good stability with less risk of acidification.