We present an innovative three stage process for advanced biodiesel production from soapstock. The advanced biodiesel synthesis scheme from SS developed in this work includes 3 following stages: Synthesis of quality AO, esterification of the AO with methanol in presence of acid catalyst and transesterification of the obtained mixture with methanol in the presence of a basic catalyst. Advanced biodiesel synthesis from low quality rapeseed oil soapstock includes simple chemical methods, inexpensive reagents and mild conditions. Obtained product shows high FAME content (94.8%) and medium overall yield (43%). Thus, the currently realized production of advanced biodiesel from used cooking oil can certainly be expanded by using the SS (by-product of refined vegetable oil production). As the world production of vegetable oil is constantly growing and now exceeds 200 million ton per year, SS can become an important raw material for expanding the production of advanced biodiesel