Microwave heating was applied to isomerize maltose to maltulose, using arginine as a catalyst. The initial molar ratio of arginine/maltose was kept constant at 0.05. Maltulose yields of 0.28–0.30 were achieved within 90–400 s, dependent on the microwave power and the volume of the substrate solution but not on the initial concentration of maltose, indicating that isomerization of maltose by microwave heating is highly productive. Independent of the power of the microwave oven and the volume of the substrate solution, the fraction of remaining maltose, the yield of maltulose, the pH of the reaction mixture, and its absorbance at 280 and 420 nm could be expressed as a function of energy density, which was defined as the amount of energy absorbed per unit volume of the reaction mixture. This indicates that the operating conditions for the isomerization of maltose to maltulose by microwave heating can be determined based on the energy density.Practical applicationsIsomerization of aldose saccharides to their rare keto‐isomers in the presence of arginine in a heated aqueous solution is a green and effective process. To further improve the process efficiency, microwave heating can be employed. This study also demonstrated that a so‐called “energy density” can be used to determine the operating condition for the isomerization of sugar by microwave heating.