This research focuses on purifying the biodiesel provided by the Davao City Biodiesel Plant using a modified fractional distillation. The researchers considered six variables to determine raw and purified biodiesel properties and characteristics: density, kinematic viscosity, flashpoint, fire point, soap content (NaOH and KOH), and water content. The experimentation results were verified using ASTM D6751 – Standards Specification for Biodiesel Fuel (B100). For the purified biodiesel, an increase in flashpoint and fire point temperatures has been observed using the modified process, thus exceeding the standard limit. Although it affects biodiesel quality, an increase in flashpoints and fire points may be better for fuel handling, transportation, and storage safety reasons. These barely influence the overall performance of biodiesel. In conclusion, the modified process improved the quality of the raw biodiesel from 50% to 83% of the variables' set standard with the optimum conditions of 3.5 inHg at 2 hours and 2.5 inHg at 1 hour.