AbstractBackground and objectivesFruit by‐products have been used as a strategy to increase the mineral content of cookies. However, to admit functionality in the organism, these minerals must be bioavailable. Therefore, this study aimed to evaluate the effect on the mineral bioavailability (calcium, iron, and zinc) of cookies prepared with partial replacement of wheat flour by fruit by‐products (melon peel, apple endocarp, and pineapple central axis).FindingsCookies containing fruit by‐products presented lower levels of phytate and oxalate when compared to the control. The use of pineapple by‐product in cookies increased zinc retention (26.40%). Cookies containing melon by‐product presented a higher uptake for iron (2.14%). Cookies with apple by‐product demonstrated the highest transport (0.06% and 9.71%) and uptake (2.92% and 15.52%) efficiencies for calcium and zinc, respectively.ConclusionsThe use of fruit by‐products in cookie formulations was associated with an improvement in the mineral bioavailability, which may represent nutritional and functional benefits for this foodstuff.Significance and noveltyAlthough some studies contemplate the use of fruit by‐products to increase the mineral content of cookies, the determination of their antinutrients and the effects on the mineral bioavailability measured by Caco‐2 cells are not widely explored in the literature.