A bio-based process oil for rubber compounds is one of the compounding ingredients to be used toward an eco-friendly and more sustainable rubber technology. This work investigates epoxidized palm oil (EPO) as an alternative for petroleum-based process oil in silica-reinforced natural rubber (NR) tire tread compounds. The effect of different incorporating steps of EPO on the properties of the rubber compounds is first studied, taking into account that the polar functional groups in the oil molecules may interact with the silanol groups on the silica surface. The properties of silica-reinforced NR compounds with EPO oil are compared with that of reference mixes with treated distillate aromatic extract (TDAE) and without oil. The compounds with EPO show a lower viscosity, filler–filler interaction, and flocculation rate constant but higher cure reaction rate constants compared with the compound with TDAE. The results indicate that the epoxide groups in EPO interact with the silanol groups on the silica surface, promoting a greater shielding effect on the polar surface and thus better silica dispersion and less interference with the vulcanization reaction. The different incorporating steps of EPO show no significant effect on the viscosity, filler–filler interaction, or flocculation rate constant but clearly affect the extent of crosslinking, as indicated by the cure torque difference. The presence of EPO in an early stage of the mixing together with the first half addition of silica and silane results in the lowest cure torque difference, modulus, and tensile strength (i.e., the highest tan δ at 60 °C), which indicates a possible obstruction for the interaction between the silanol groups and silane coupling agent by the EPO molecules. Comparing EPO with different epoxide contents in the range of 1–3 mol%, the increase in epoxide content gives similar Payne effects but enhances the cure reaction, resulting in improved tensile properties and tan δ at 60 °C. The results clearly prove that EPO can be used as a TDAE alternative.