The exhaustion of natural resources has increased petroleum prices and the environmental impact of oil has stimulated the search for an alternative source of energy such as biodiesel. Waste cooking oil is a potential replacement for vegetable oils in the production of biodiesel. Biodiesel is synthesized by direct transesterification of vegetable oils, which is controlled by several inputs or process variables, including the dosage of catalyst, process temperature, mixing speed, mixing time, humidity and impurities of waste cooking oil that was studied in this case. Yield, turbidity, density, viscosity and higher heating value are considered as outputs. This paper used multi-response surface methodology (MRS) with desirability functions to find the best combination of input variables used in the transesterification reactions to improve the production of biodiesel. In this case, several biodiesel optimization scenarios have been proposed. They are based on a desire to improve the biodiesel yield and the higher heating value, while decreasing the viscosity, density and turbidity. The results demonstrated that, although waste cooking oil was collected from various sources, the dosage of catalyst is one of the most important variables in the yield of biodiesel production, whereas the viscosity obtained was similar in all samples of the biodiesel that was studied.