Abstract The kinetics of the alkali-catalyzed transesterification of sunflower oil with methanol in the presence of co-solvent (TSMPC) were investigated. The kinetics curves of the alkali-catalyzed TSMPC, in the temperature range of 26°C–55°C, were measured for conventional heating (CH) and microwave heating with controlled cooling. The results showed that for both heating modes, the kinetics of the alkali-catalyzed TSMPC reaction can be described with the kinetic model of the pseudo first-order reaction with respect to the concentration of the triglycerides. The values of apparent reaction rate constants, activation energies, and pre-exponential factors are also calculated. The existence of a linear correlation (compensation effect) between the values of apparent kinetic parameters determined for CH and microwave heating with controlled cooling conditions is established. The results confirmed that the increase in the transesterification rate in the microwave heating with controlled cooling conditions is not caused by overheating nor by the existence of hotspots. The model of mechanism of the impact of microwave heating on the kinetics of transesterification is hereby proposed.