Using calcium oxide-based catalyst, optimization of two-stage trans-esterification processes at a fixed catalyst (1.0 wt. %) and molar ratio (1:6) was achieved. Processes were tested on Jatropha, Sweet Almond and Sesame seed oils to produce and compare biodiesel yields. An optimization solution of speed (629.630 rpm), temperature (26.661 oC), and time (60 min) resulted in an 83.304% for refined jatropha biodiesel (RJB) production, with an overall attractiveness of 0.853. The expected optimal yield rates of 86.915–90% obtained from various models were higher than the ASTM D 6751 and EN 14214 standards, which both required an experimental range of 46–55 % in conventional biodiesel production. The effects of speed and temperature on biodiesel yield from the refined jatropha oil (RJO), refined sweet almond oil (RSAO), and refined sesame oil (RSO) were major parameters that greatly influenced the yield, although time only changed the yield moderately.