The objective of this study was to screen the factors that affect H₂, organic acids and alcohols production from coffee waste pretreated in a hydrothermal reactor applying consortium of bacteria and fungi (indigenous from coffee waste) with hydrolytic and fermentative activity. The effects of pH (4.0–7.0), temperature (30–50 °C), agitation (0–180 rpm), headspace (50–70%), percentage of bioaugmentation (without microbial consortium to 20%), concentration of coffee pulp and husk (2–6 g/L), coffee processing wastewater (7-30 gCOD/L) and yeast extract (0–2 g/L) were evaluated using a Plackett-Burman design. The highest H₂ production potential (82 ml H₂) was obtained under the following conditions: 30 °C, 180 rpm, 50% headspace, without bioaugmentation, 2 g/L pulp and husk coffee, 30 gCOD/L coffee processing wastewater and 2 g/L yeast extract. The main soluble products were acetic acid (1956 mg/L), lactic acid (786 mg/L) and ethanol (816 mg/L). Lactobacillus sp., Clostridium sp., Saccharomyces sp. and Kazachstania sp. were the main autochthonous microorganisms identified. Through metagenome functional analysis, enzymes related to lignin, phenol, cellulose, lignocellulose, and pectin degradation were identified, as well as acidogenesis, and H₂ production.