The objective of this study was to determine the effects on quality of incorporating raspberry and cranberry pomaces into American-style muffins prepared under various baking conditions. The different baking conditions did not affect the texture or microstructure of the control muffins. The enhanced samples baked at 140 °C for 30 min were characterized by a harder texture than the control muffins and by a distributed protein matrix and distorted starch granules, while those baked at 240 °C for 15 min had a moist texture and showed incomplete starch gelatinization. The mean percent recovery of ellagic acid, flavonols, tocopherols, tocotrienols, and anthocyanins after baking were 156, 53, 48, 43, and 22 %, respectively. Lower baking temperature was better for ellagic acid and tocotrienols, but worse for flavonols, tocopherols, and anthocyanins. It seems that, for the enhanced samples, the intermediate baking conditions (180 °C for 20 min) guarantee the best microstructure and texture and the appropriate retention of phytochemicals in muffins.