In this work, an autohydrolysis treatment was applied to cocoa bean shells (CBS) to obtain different potentially added-value fractions rich in phenolic compounds with antioxidant potential and oligosaccharides with potential prebiotic properties. The final residue was enzymatically treated to deliver sugars that can undergo fermentation-based biotransformation. This hydrothermal pretreatment was assessed for maximum temperatures (Tmax) between 120 to 200 °C and severities (S0) between 1.1 and 3.4. The highest oligosaccharide concentration (5.5 g/L) was achieved at S0 of 3.4. The increase of S0 during the process allowed to increase the recovery of interesting bioactive compounds, achieving a maximum TPC and antioxidant activity of 2.8 g/L and 17178.5 µmol Fe2+/L, respectively, when the Tmax reached 200 °C. However, at this temperature, a significant amount of degradation products such as organic acids and HMF was already formed, and a compromise temperature of 160 °C was chosen for further tests. It was possible to obtain a maximum glucose yield of 71% when the pretreated solids were enzymatically hydrolysed. Hence, the use of autohydrolysis, avoiding the use of toxic chemicals, has proved to be a sustainable alternative to obtain different CBS fractions with interesting composition to be potentially employed in multiple sectors.