In this paper, a comparative study of the separation and purification of biodiesel and crude glycerol obtained by transesterification of rapeseed oil with methanol using NaOH, CaO and calcium glyceroxide as catalysts has been conducted. For isolation and purification of the transesterification products, a method based on neutralization of the reaction mixture with phosphoric acid, followed by separation, methanol stripping from glycerol phase and vacuum distillation of fatty acid methyl esters (FAMEs), was proposed. It has been found that by using calcium glyceroxide, the isolation and purification stage of commercial FAMEs requires less energy consumption. Moreover, less waste is formed when calcium glyceroxide was used. It has been shown that by using calcium glyceroxide as transesterification catalyst, the resulting crude glycerol is slightly colored and characterized by a a lower water content (about 0.2 wt%) and a lower ash content (about 0.3 wt%), which significantly reduces the cost of its processing. Based on the investigation results, the flow chart of the operations for the separation and purification of commercial FAMEs and crude glycerol has been proposed. The implementation of the developed purification scheme allows obtaining FAMEs, which significantly exceeding the requirements of ASTM D6751. At the same time, distilled FAMEs satisfy the requirements of ASTM D1045-14 and can be used as polyvinyl chloride (PVC) plasticizers.