This work studied the catalytic activity and stability of Ni-MoS₂ supported on γ-Al₂O₃, SiO₂, and TiO₂ toward deoxygenation of different feedstocks, i.e., crude Pongamia pinnata oil (PPO) and refined palm olein (RPO). PPO was used as a renewable feedstock for bio-hydrogenated diesel production via catalytic hydrotreating under a temperature of 330 °C, H₂ pressure of 50 bar, WHSV of 1.5 h⁻¹, and H₂/oil (v/v) of 1000 cm³/cm³ under continuous operation. The oil yield from a Soxhlet extraction of PPO was up to 26 wt.% on a dry basis, mainly consisting of C18 fatty acids. The catalytic activity in terms of conversion and diesel yield was in the same trend as increasing in the order of NiMo/γ-Al₂O₃ > NiMo/TiO₂ > NiMo/SiO₂. The hydrodeoxygenation (HDO) activity was more favorable over the sulfided NiMo supported on γ-Al₂O₃ and TiO₂, while a high DCO was observed over the sulfided NiMo/SiO₂ catalyst, which related to the properties of the support material and the intensity of metal–support interaction. The deactivation of NiMo/SiO₂ and NiMo/TiO₂ occurred in a short period, due to the phosphorus and alkali impurities in PPO which were not found in the case of RPO. NiMo/γ-Al₂O₃ exhibited the high resistance of impure feedstock with excellent stability. This indicates that the catalytic performance is influenced by the purity of the feedstock as well as the characteristics of the catalysts.