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This work investigated the application of a thermophilic (55 °C) anaerobic reactor with immobilized biomass, mechanically stirred and operated in sequential batch and fed batch (AnSBBR) for environmental compliance and methane production by co-digesting cheese whey (W) and sugarcane vinasse (V). The assays were performed in four steps. In the first step the composition of 75%W:25%V (on a COD basis) was determined to be the most adequate for the anaerobic process. In the second step the applied volumetric organic load (AVOL) was increased and in the third step the feed strategy was modified achieving best results at AVOL of 25 gCOD.m−3.d−1, in which the removed organic matter efficiency was 72%, the molar productivity was 278 molCH 4.m−3.d−1 and methane yield was 15.3 mmolCH 4.gCOD−1. In the fourth step the temperature was modified to 50 °C and 45 °C, achieving worse results. From the kinetic model adjusted to experimental data it was identified that the acetoclastic route was predominant in methane generation. The estimated energy recovered by co-digesting cheese whey and sugarcane vinasse using industrial information was 2.2 × 104 MW h per month, equivalent (in Brazil) to the electricity consumption of about 135 × 103 inhabitants or monthly savings of US$ 1,653,000 replacing the diesel oil consumed in the industry. • Viability of a thermophilic system producing CH 4 from sugarcane vinasse and whey. • Highest CH 4 productivity: 278 molCH 4.m−3.d−1. • Best wastewater composition of 75 %Vinasse:25% Whey. • Best operational strategy: 25 kgCOD.m−3.d−1 and fed batch-mode. • Energy yield of the system: 2.2 × 104 MW h.month−1. [ABSTRACT FROM AUTHOR]