Transition metal carbides have emerged as an attractive alternative to conventional catalysts in hydrodeoxygenation (HDO) reactions due to surface reactivity, catalytic activity, and thermodynamic stability similar to those of noble metals. In this study, the impact of varying Mo concentration in carbon nanofiber-supported catalysts for the supercritical ethanol-assisted HDO of bio-oils in an autoclave batch reactor is discussed. Raw bio-oils derived from agave bagasse and corncob through solar hydrothermal liquefaction were treated at 350 °C. Our findings indicate that the presence of Mo has a strong impact on both product yield and chemical properties. Thus, a Mo concentration of 10 wt.% is enough to obtain high deoxygenation values (69–72%), resulting in a yield of upgraded bio-oil ranging between 49.9 and 60.4%, depending on the feedstock used, with an energy content of around 35 MJ/kg. A further increase in the Mo loadings (20 and 30 wt.%) reduced the loss of carbon due to gasification and improved the bio-oil yields up to 62.6 and 67.4%, without compromising the product quality.