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Triacylglycerides (TAGs) produced via the syngas fermentation of biogenic residues and wastes were evaluated as a potential feedstock for advanced road transportation, aviation, and maritime drop-in fuels via hydroprocessing technology. Due to the limited availability of TAGs, a simulated feedstock (SM TAGs) was utilized by blending various commercial oils, simulating the fatty acid composition of TAGs. At first, the simulated feedstock and the real TAGs were hydrotreated on a TRL 4 (technology readiness level) pilot plant to evaluate the potential of the SM feedstock to simulate the TAGs based on product quality. The hydrotreatment technology was evaluated and optimized on a TRL 4 plant. The research was further extended to a TRL 5 hydrotreatment plant with the optimum operating window for scaling up the technology. The resulting product was fractionated on a batch fractionation unit under vacuum to separate the jet and diesel fractions. The produced fuels were analyzed and evaluated based on the aviation Jet A1, EN590, EN15940, and marine diesel DMA specifications. The results show that the TAG composition was successfully simulated via a blend of vegetable oils. In addition, the hydrotreatment of the real TAGs and simulated feedstock resulted in similar-quality liquid products. The technology was successfully scaled up on a TRL 5 unit, leading to advanced, high-quality aviation and diesel drop-in fuels from TAGs, while the reaction pathways of hydrotreating can be controlled via the operating parameters of pressure, temperature, and H2/oil ratio. The hydrotreatment process’s optimum conditions were 13.8 MPa pressure, 643 K temperature, 1 h−1 liquid hourly space velocity (LHSV), and 5000 scfb hydrogen-to-oil ratio. Finally, a storage stability study of the hydrotreated liquid product showed that it can be stored for more than 6 months at ambient conditions without any noticeable changes to its properties.