Cookies, which form the largest category of bakery snacks, are considered a good vehicle to introduce nutrients into the diet. In this study, to increase the nutritional value of traditional commercial cookies, wheat flour was substituted with defatted flours made from flax, sesame, chia, and poppy, which are byproducts of the oil extraction industry. The differences in the technological properties, nutritional composition, and consumer acceptance of the reformulated cookies were evaluated. The results show that the wheat cookies used as the control showed a more elastic behavior than the cookies elaborated with defatted seed flours, which showed a greater tendency to crumble. The use of defatted seed flours yielded cookies with a higher content of protein and fiber, and a lower content in carbohydrates than the wheat cookies. Consumer evaluations for the sesame and flax cookies were similar to those for the traditional wheat cookies, with positive assessments on all of the parameters evaluated. On the other hand, the cookies elaborated using chia and poppy flours received the least positive evaluations from consumers. Thus, the use of some defatted seed flours, mainly flax and sesame, is proposed as an interesting alternative to produce health-promoting cookies in order to cover the current demand for gluten-free products.