Traditional biodiesel production technologies are complex, energy consuming and lead to the formation of by-products, such as glycerol phase and waste water during biodiesel washing. The paper deals with improving the technology of biodiesel production by treating rapeseed oil with an emulsifier to obtain a microemulsion of oil and ethanol, which do not mix with each other. The use of excess sodium ethoxide allows to transesterify both rapeseed oil and glycerol, which is a by-product of traditional technologies. The esterification products of glycerol are ethyl glycerates. Biodiesel, containing ethyl ethers of glycerol, has better performance properties. The technological scheme of such a process does not require the separation stage of glycerol and biodiesel phases. However, this product should be thoroughly cleaned. Therefore, a centrifuge was added to the technological scheme. The new technological scheme of the process makes it possible to improve the technology of biodiesel synthesis. The traditional technology of biodiesel production involves cooling and draining the wash water into the sewer, which is unacceptable in the modern conditions of environmental pollution. The paper considers the solution to the problem of wastewaters that accumulate after the washing phase. They contain the residues of salts, sulfuric acid, ethyl alcohol and emulsifier neonol, which form a stable azeotropic mixture. The traces of ethyl alcohol can be removed by simple distillation. However, removing other components requires the use of advanced methods. To reduce pollution in the wash water, the approbatory studies of the effective physico-electrochemical technology were performed by means of treating water in an electrical device before it was directed to a thin-layer settling tank and then to the filtration through zeolite. This purification technology helps to increase the purification degree in terms of chemical oxygen demand (COD) from 86.8 to 92.5 that proves reducing pollutants entering the environment. The proposed improvements of biodiesel technology help to increase the yield of biodiesel due to the esterification of glycerol and make the process more environmentally friendly