Abstract Solid waste (pulp and husk) and wastewater from post-harvest coffee processing contain high carbohydrate content, which can be used in biofuel production. However, the recalcitrance of lignocellulosic material in the pulp and husk, in addition to the polyphenols in wastewater limits its application. The objective of this research was to evaluate the coffee processing waste for H2 production. The experiments were carried out in batch reactors analyzing the co-digestion of: (1) wastewater with pulp and husk in natura or ground, (2) pulp and husk pretreated in the hydrothermal system and (3) liquid fraction from pretreatment of the pulp and husk in the hydrothermal system. The severity factor of the pulp and husk hydrothermal pretreatment was between 3.2 and 4.2, in addition to bioaugmentation of the autochthonous consortium (bacteria and fungi) from the waste. The highest H2 production potential of 8 mL was obtained by co-digestion of pretreated pulp and husk in severity 3.5 with coffee processing wastewater. Pulp and husk pretreatment with the hydrothermal system at 180 °C for 15 min favored in increased 20% cellulose, 14% hemicellulose, and 31% lignin. Hydrothermal pretreatment and waste co-digestion improved up to 7 times the H2 production when compared to in natura waste.