An efficient purification of biodiesel from glycerol (Gl) as a byproduct is a critical task for optimizing its production. This study focuses on investigating the efficiency of glycerol extraction from five model biodiesel systems (methyl butyrate, methyl hexanoate, methyl octanoate, methyl decanoate, and methyl laurate) using deep eutectic solvents (DES) based on choline chloride (ChCl)/glycerol and choline chloride/urea (Ur). The influence of DES composition (choline chloride/glycerol) on the separation efficiency was evaluated. Methanol remaining after synthesis was also extracted from the model system using DES. With an increase in the carbon chain length of the ester in the model system, the amount of residual glycerol after synthesis decreases. It was demonstrated that extraction with both DES reduces the amount of glycerol (<0.001 mole fraction) in the model system by an order of magnitude. Additionally, a deficit of glycerol in DES increases extraction efficiency. Repeated extraction allowed complete removal of residual glycerol from all model systems studied. For DES (choline chloride/urea), distribution coefficients for glycerol and methanol were calculated, confirming good separation efficiency. It is shown that the maximum distribution coefficient for glycerol and methanol is achieved in the experiment with methyl laurate, which is equal to 193 and 2.53, respectively.