There is increasing interest in the production of biodiesel from non-edible oil sources such as waste or recycled oil and animal fats. Transesterification is the most commonly used method to convert triglycerides (TG) from different types of lipids. After reviewing the range of available feedstocks, this chapter uses thermodynamic analysis to investigate the main three transesterification reaction systems: triolein and supercritical methanol (T&SCM), triolein and supercritical ethanol (T&SCE), and triolein and supercritical isopropanol (T&SCI). Using a case study, it identifies ways of optimizing supercritical transesterification technology for biodiesel production, as well as ways of improving the quality of the biodiesel manufactured from the process.