In coffee-producing countries such as Colombia, Coffee Cut-Stems (CCS) as waste is abundant, either from cuts or renovation. On average, 17 tonnes of dry wood per hectare can be obtained from the renovation. These residues would serve to produce, approximately, 690 GWe every year; however, the energy content of these residues is not properly used and the direct emissions related to their combustion are relatively high. Based on this statement, this paper performs the techno-economic, energetic and environmental assessment for hydrogen production through dark fermentation using CCS as raw material aiming to improve the economic valorization of this wood waste. Low productivities, low energy performance, and high environmental impacts are obtained when considering the stand-alone production of hydrogen; nevertheless, the energetic valorization of by-products (ethanol, acetic acid and butyric acid) improved the profitability, energy performance and environmental impacts of the process scheme. Therefore, it is very understandable that the stand-alone ways for hydrogen production are not yet the solution, and different approaches should be included such as the integrated biorefinery pathways.