The effects of adding vinasse (VIN) as a co-substrate on the stability and production of volatile fatty acids (VFA) and methane (CH4) during the anaerobic digestion (AD) of microalgal biomass (MB) were evaluated. The AD system consisted of an acidogenic reactor (AR) followed by a methanogenic reactor (MR). The experiment was divided into phase I-start-up and AD of VIN; phase II-MB+VIN co-digestion (50:50 based on chemical oxygen demand (COD)); and phase III-co-digestion of pretreated MB and VIN (PTMB+VIN, 50:50). In phase I, the total amount of VFA in the AR increased from 240 to 2126 mg/L. In the MR, the conversion of VFA into CH4 yielded an average of 71 ± 37 NmL CH4/g CODin. In phase II, the initial CH4 production was 246 ± 31 mL CH4/g CODin but it decreased to 63 mL CH4/g CODin due to the accumulation of longer chain acids. More stable conditions were achieved after two hydraulic retention cycles and the average CH4 yield in this phase was 183 mL CH4/g CODin. In phase III, when using PTMB, 197 ± 72 NmL CH4/g CODin were obtained, i.e., a 2.7- and 1.1-fold increases compared to phases I and II, respectively. The predominance of acetate producers and syntrophic organisms suggests acetoclastic methanogenesis, confirmed by the occurrence of Methanosaeta (10.5%).