International reports warn us about our growing reliance on petroleum, driving up the demand for fossil fuels to unsustainable levels in order to meet global energy needs. The core work of this study is to modify an existing biodiesel prototype through aeration and condensation. Initiatives had been made on the development of technologies for sourcing out additional sources of energy considering conversion of waste to fuel. Meanwhile, there are attempts to convert waste cooking oil to biodiesel through a transesterification biodiesel reactor. Unfortunately, the biodiesel derived from such was not compliant with the existing standards for the pure and blended biodiesel specifically on the moisture content. In that notion, the core work of this study is to modify an existing biodiesel prototype, which includes modification of the reactor tank, and the addition of several important design elements such as an agitator, condenser, and an oil tank with built-in filtration system. Fabricate the remodeled prototype, produce commercial-grade biodiesel, perform analyses on the product’s properties, and conduct assessments for the real-life applications of the produced biodiesel. The addition of auxiliary components was proven significant as the moisture content of the biodiesel produced after the modification is significantly lower in comparison with that of the previous results. It was also determined that the optimized conditions that would result in the highest yield are as follows: 6:1 methanol-oil ratio, 3 h of aeration time, and 3 h of condensation time. Analysis of the product also presents that except for the FAME and water content and flash point, both of which show slight deviation, all the properties of produced pure and blended biodiesel conform to the Philippine National Standards for Coco Methyl Ester.