BACKGROUND Food processing produces large volumes of waste that can be transformed into useful and relevant ingredients. The by‐product of oil extraction from faveleira seeds is a potentially low‐cost raw material that can be used for obtaining functional foods. This study aimed to analyze the physicochemical properties, chemical composition, and antioxidant activity of faveleira (Cnidoscolus quercifolius Pohl) seed press cake flour (FSPCF). Additionally, the chemical composition, antioxidant activity, and physical, microbiological, and sensory aspects of cookies with 0, 25%, or 50% substitution of refined wheat flour (RWF) with FSPCF (0‐FSPCF, 25‐FSPCF, and 50‐FSPCF cookies, respectively) were evaluated. RESULTS FSPCF exhibited good physicochemical properties, high antioxidant activity (0.45 ± 0.00 and 42.83 ± 1.30 g TE g−1 for the DPPH and ABTS methods, respectively), and high polyphenol content (particularly gallic acid at 21015.85 ± 4981.76 g kg−1) and is also rich in minerals and fiber (359.40 ± 1.10 g kg−1). Replacement of RWF with FSPCF increased the activity of antioxidants and the levels of polyphenols, ash, lipids, proteins, and fibers. The 50‐FSPCF cookie possessed the highest linoleic acid content (97.50 ± 8.47 g kg−1). Flour replacement influenced the weight of the cookies without affecting the other physical characteristics. The cookies yielded good sensory acceptance and purchase intentions. Contamination was not detected. CONCLUSION Faveleira flour possesses high nutritional and bioactive value and can be used as a functional ingredient in cookies and possibly in other bakery products such as bread, cakes, and pastas. © 2022 Society of Chemical Industry.