Developing high-efficiency, high-stability, and low-cost deoxygenation and hydrocracking catalysts could be considered one of the most significant breakthroughs in catalytic hydroprocessing. The present study utilized aluminophosphate (AlPO4-18), a zeolite-like molecular sieve, as catalyst support for producing carbon-coated β-Mo2C, Ni3C, and WC nanoparticles. The synthesis used an incipient wetness impregnation followed by a temperature-programmed reduction-carburization approach which involved cracking a hydrocarbon gas, propane, in a hydrogen environment. The synthesis parameters were a 1:7 propane/hydrogen reductive-carburizing gas stream, 15 wt.% metal loading, an 800 °C carburization temperature ramped-up at a heating rate of 10 °C min−1, a 2-h holding time, and a 1-h holding time in hydrogen. The synthesized catalysts were characterized using thermogravimetry mass spectroscopy/temperature-programmed oxidation (TPO TG-MS), nitrogen physisorption at 77 K, X-ray diffraction (XRD), and transmission electron microscopy/energy-dispersive X-ray spectroscopy (TEM EDS). TPO TG-MS, nitrogen physisorption, TEM, and XRD characterization results proved that atomic carbon was successfully incorporated into the lattice interstitials, resulting in thermally stable, well-dispersed, crystalline and mesoporous β-Mo2C/AlPO4-18, Ni3C/AlPO4-18, and WC/AlPO4-18 nanoparticles. XRD analysis showed structural evolution during reduction-carburization, with average crystallite sizes of metal-containing particles of 8.2–9.22, 6.64–8.50, and 6.03–7.56 nm for β-Mo2C/AlPO4-18, Ni3C/AlPO4-18, and WC/AlPO4-18, respectively. These values did not significantly deviate from high-resolution TEM analysis. The surface areas of the nanoparticles were categorized in decreasing order as WC/AlPO4-18 > Ni3C/AlPO4-18 > β-Mo2C/AlPO4-18, with values of 193.79, 169.05, and 66.57 m2 g−1, respectively. In conclusion, these carbon-coated metal carbide nanoparticles with excellent thermal, structural, microscopic, and textural properties can be viable alternatives to noble metal catalysts for producing bio-jet fuel using the hydroprocessing pathway.