The management of coffee and peapod waste presents significant environmental challenges, with millions of tons generated annually, leading to disposal issues and resource inefficiencies. Hydrothermal processes offer a promising valorization method, though biomass characteristics significantly influence the resulting products. Biomass characterization revealed distinct profiles for coffee cherry waste (moisture: 10.94%, ashes: 7.79%, volatile matter: 79.91%, fixed carbon: 1.36%, cellulose: 27.6%, hemicellulose: 12.5%, and lignin: 13.7%) and peapods (moisture: 7.77%, ashes: 4.22%, volatile matter: 74.18%, fixed carbon: 13.0%, cellulose: 20.2%, hemicellulose: 17.4%, and lignin: 5.0%). Experiments were conducted in 100 mL and 500 mL hydrothermal reactors with varying conditions for temperature (120–260 °C), time (1–4 h), stirring (none and at 5000 and 8000 rpm), biomass/water ratio (1:5, 1:10, 1:20, and 1:40), particle size (0.5–5 mm), and catalysts (acids and bases). The results showed that peapods produced over 30 times more platform chemicals than coffee. High temperatures (over 180 °C) degraded peapods, whereas coffee yields increased. Both biomasses were influenced similarly by reaction conditions: lower biomass/water ratios, smaller particle sizes, acid catalysts, and no stirring increased yields. Peapods consistently had higher yields than coffee in all conditions. Biochar analysis revealed anthracite from coffee and coal from peapods.