This work presents an alternative bioenergy-related management approach for sugarcane molasses through the application of anaerobic digestion (AD) in a two-stage continuous thermophilic (55 °C) system to produce biohydrogen (bioH2) and methane. The performance of the acidogenic stage (RH2) was assessed by maintaining a continuous and high organic loading rate (OLR; 120 kg COD m−3 d−1), whilst the robustness of the methanogenic stage (RCH4) was investigated based on the increase of the OLR (1.0–25.2 kg COD m−3 d−1). Molecular analyses and an energetic assessment were also conducted, to provide a holistic understanding of the two-stage AD system. Long-term bioH2 production was achieved at low pH values (~4.0) in RH2 by the co-fermentation of lactate and acetate, and a positive correlation between Clostridium and Leuconostoc genera was identified. Efficient methane production (323–350 NmL CH4 g−1COD) was only observed at low OLR (1.0–2.3 kg COD m−3 d−1) in RCH4, although high COD removal levels (>70%) were observed at all operational conditions. Metabolite and molecular analyses indicated inefficient syntrophic and acetoclastic activities (accumulation of acetate, propionate and lactate), indicating that hydrogenotrophic methanogenesis was the prevailing methane-producing pathway in RCH4, specifically by the Methanothermobacter genus. Finally, the energetic potential (8560 kJ kg−1CODapplied) of molasses outperformed the ones of vinasse by at least 25%, indicating that the high availability of biodegradable organic matter in molasses requires a low OLR to offer efficient bioenergy recovery levels.