Abstract Hierarchical zeolites containing ruthenium oxide nanoparticles were applied in the reaction of dihydroxyacetone isomerization to alkyl lactates and lactic acid. The synthesis of these materials was performed by dispersing the specified amount of two microporous zeolites (HFAU and NaBEA) withan ultrasound bath for 30 min, in a mixture containing cetyltrimethylammonium bromide, water, ethanol and ammonia. Then, tetraethyl orthosilicate and a source of ruthenium, were added and subjected to mixing for 4 h at 65 °C. The synthesized zeolites displaying secondary porosity in the range of mesopores were characterized by using a series of measurement techniques: XRD, SEM/EDX, TEM, low temperature adsorption/desorption of nitrogen. The reaction of triose isomerization, in this case dihydroxyacetone, was conducted by means of two methods, i.e., with the use of conventional heating and microwave radiation. The application of microwave radiation allowed for reduction of the reaction time to 1 h and accomplishing high dihydroxyacetone conversion (>90%) and high yields of the desired reaction products (>80%). Methanol, ethanol and water were used as reaction media.