Products of the reaction include not only biodiesel, but also the byproducts soap, glycerol, excess alcohol, and trace amounts of water. All of these byproducts must be removed to meet the standards, but the order of removal is process-dependent.
The density of glycerol is greater than that of biodiesel, and this property difference is exploited to separate the bulk of the glycerol coproduct. Residual methanol is typically recovered by distillation and reused. Soaps can be removed or converted into acids. Residual water is also removed from the fuel.