The aim of this work was to improve the antioxidant quality of cookies using defatted chia flour (DCF), which is a by- product of the food industry. We prepared cookies containing DFC (5, 10 and 20%), and evaluated the technological and sensory qualifies of cookies. Additionally, we verified the effects of processing and simulated gastrointestinal digestion on polyphenols content. The addition of DFC did not affect the technological quality of cookies, with the exception of color. Furthermore, cookies supplemented with 10% DFC were sensorial preferred over the others. The addition of DFC increased the polyphenol content and the in vitro antioxidant capacity of cookies. Besides, the simulated gastrointestinal digestion suggested that 73% of total polyphenols could be absorbed in the intestine, showing an antioxidant effect greater than expected, also showing prebiotic effects. Supplementation of cookies with 10% DFC could be recommended to improve antioxidant quality without reducing the technological or sensorial properties.