Anaerobic digestion (AD) of residues from integrated first- and second-generation ethanol (1G2G) biorefineries is a sustainable method for energy recovery through biogas production. This study evaluated the co-digestion of 1G vinasse, 2G vinasse and pentose liquor (from the pretreatment of sugarcane bagasse for 2G ethanol production) compared to individual digestions using biochemical methane potential (BMP) assays. The results showed some “key” micronutrients from the substrates that affected methane (CH₄) production, while their balance provided by co-digestion achieved high digestibility (95%). High iron (Fe) and nickel (Ni) concentrations, in addition to furfural (0.33 g L⁻¹) in pentose liquor seemed to decrease its CH₄ production potential. Despite these adverse effects observed in mono-digestion, co-digestion was beneficial for this substrate, increasing digestibility (52%) and BMP (118%). The highest BMP was observed in vinasse 2G (631 ± 6 NmL CH₄ gTVS⁻¹), with no significant difference compared to the adjusted modified Gompertz model (624 ± 10 NmL CH₄ gTVS⁻¹). The co-digestion system also presented the highest specific CH₄ production rate (20 ± 1 NmL CH₄ gTVS⁻¹day⁻¹) and shortened the lag phase by 19% compared to the AD of isolated 1G vinasse with the second lowest BMP value (494 ± 11 NmL CH₄ gTVS⁻¹).