Biodiesel is a remarkable alternative to the decreasing resources for fossil fuels. One of the critical steps in producing biodiesel is its purification from the byproduct glycerol. The content of glycerol permissible must pass the EN 14214 and ASTM D6751 international biodiesel standards. In this work, methyl triphenyl phosphunium bromide as salt and three different hydrogen-bond donors, namely, glycerol, ethylene glycol, and triethylene glycol, were selected to synthesize three deep eutectic solvents (DESs). These DESs were employed as the solvent for the removal of glycerol from palm-oil-based biodiesel. The effects of DES type on the removal of free glycerol, bound glycerol, and total glycerol were investigated. The results revealed that the ethylene glycol DESs and triethylene glycol DESs were successful in removing all free glycerol from the palm-oil-based biodiesel. All tested DESs were able to reduce the content of monoglycerides (MGs) and diglycerides (DGs). Moreover, all used DESs had the tendency to reduce the DGs more effectively than removing MGs. The maximum removal efficiency of MGs and DGs was attained by triethylene-glycol-based DESs at a molar ratio of 3:1 (DES8:biodiesel) and 0.75:1 (DES8:biodiesel), with 37.9 and 53.4% removal, respectively. The total glycerol was reduced below the ASTM standards using all tested DESs. The DES:biodiesel molar ratios of 3:1 for DES4 and 3:1 for DES8 were found to be the most effective solvents for reducing total glycerol content, with 40 and 50% removal efficiency, respectively.