Hydrothermal carbonization (HTC) of low quality, wet biogenic residues into intermediate bioenergy carriers can potentially contribute to a more flexible and stable renewable energy system and reduce environmental impacts compared to current residue disposal practices. This study quantifies the environmental impacts via life cycle assessment (LCA) of a novel hydrothermal process for the treatment on an industrial scale of application of three wet biogenic residues (paper bio-sludge, olive pomace, and orange peel) into bioenergy carriers, i.e., solid pellets and biogas. A comprehensive attributional cradle-to-gate life cycle assessment (LCA) was conducted; the life cycle impact assessment (LCIA) utilised the ReCiPe impact assessment method. A selection of 10 significant impact categories was prioritised. Reliability of this categorization was also ensured through a sensitivity analysis carried out using Monte Carlo simulation. Climate change, particulate matter formation and terrestrial acidification impact categories showed the highest reliability, while for freshwater ecotoxicity and freshwater eutrophication impact categories in the study suggest the need for more robust data and further investigation. The climate change impact category presents the following values, as kg CO2eq/tresidue: pulp and paper bio-sludge (PPB), 17.9; olive pomace (OP), −1290; orange peel (ORP), −1301. The LCA study compared electricity yields of the hydrothermal treatment process with conventional treatment processes for each of the target residue streams. The environmental performance of the proposed hydrothermal treatment benefits significantly from the combination of intermediate bioenergy carriers (pellets) from the solid fraction with biogas production from the liquid fraction. Avoided emissions due to the heat recovery provide further environmental benefits. The LCIA results show that the carbon footprint of the F-CUBED production system, as kgCO2eq/kWhe, accounts for –4.56, −0.63, and −0.25 for paper bio-sludge, olive pomace and orange peel, respectively.