The effect of microwave (MW) treatment with different power densities (4.4, 7.7, and 11.0 W/g) on polyphenol oxidase (PPO) and pectin methyl esterase (PME) inactivation in peach puree were studied, and the changes in color, rheological properties, total polyphenol and flavonoid and antioxidant capacity were evaluated. By using time/temperature data collected during MW heating, three cook values levels (0.36, 10, 24 min) for each power density were calculated. The PPO was significantly decreased from ca. 50% to ca. 5% when increasing the cook value level, regardless of power density applied. While PME significantly decreased from 40.6% to 10.2% when power density increased from 4.4 to 11.0 W/g at cook value 24 min. MW treatment did not alter the flow behaviour of peach puree. The apparent viscosity values of peach puree significantly increased after MW treatment with increasing cook value, regardless of power density applied. The L* values of peach puree significantly increased from 36.98 to 38.10 or more after MW treatment at cook value 10 min and 24 min. MW treatment could maintain the amount of total polyphenol, total flavonoid and antioxidant capacity, preserving the nutritional and functional values of the product.