This study aimed to compare ozone-microbubble-washing (OM) performed by domestic equipment with conventional water-washing (CW) regarding resultant quality attributes of muscle foods. For this purpose, muscle microstructure and lipid and protein oxidation were evaluated in pork and fish samples after OM and CW treatments. The assessment of muscle microstructure showed that OM treatment did not damage the microstructure of muscle fibers in both pork and fish samples. Thiobarbituric acid reactive substances (TBARS) values were not detected in both treatment groups, and they were substantially below the generally acceptable threshold (1 mg MDA/kg). The methylglyoxal (MGO) level of OM-treated fish samples was significantly higher than that of CW-treated fish samples. However, glyoxal (GO) and MGO levels of OM-treated pork samples were significantly lower than that of CW-treated pork samples. Similar types and sites of oxidative modification and similar numbers of modified peptides, as well as no significant difference in the concentration of total and most of the free amino acids (FAA) between treatment groups, indicated that OM treatment did not accelerate protein oxidation.