BACKGROUNDThis study aimed to produce new functional cookies with high nutritional properties and low calorie content. It investigated the effects of incorporating wheat germ flour (WGF) at levels of 10–30% as a substitute for whole wheat flour (WWF), along with coffee silver skin (CSS) in the same proportions, serving as natural functional additives to substitute for fat in cookie formulations.RESULTSThe total phenol content of the cookies with added WGF‐CSS ranged from 1813.72 to 1838.45 mg gallic acid equivalent (GAE) per kilogram of dry weight (mg GAE kg−1), whereas the total phenolic bioaccessibility values ranged between 53.39 and 56.84%. Of the three methods used to determine antioxidant capacity (AC), the cupric reducing antioxidant capacity (CUPRAC) method gave higher bioaccessibility values (44.55–51.19%) than the 2,2′‐azino‐bis (3‐ethylbenzthiazoline‐6‐sulfonic acid) (ABTS) radical cation and 2,2‐diphenyl‐1‐picrylhidrazyl (DPPH) scavenging methods. The contribution of WGF‐CSS supplemented cookies to the recommended dietary allowances (RDA) (%) of K, P, Mg, and Ca increased depending on the number of cookies consumed and the WGF and CSS ratio. The general acceptability scores of the cookies varied between 5.66 and −7.08, and the 10% WGF cookie (F2) (6.48) sample received the score that was closest to that of the control. Moderately strong positive relationships (r > 0.90, P < 0.05) were detected between the physicochemical and sensory characteristics of the cookies.CONCLUSIONAs a result, WGF and CSS food additives with high nutritional properties can be recommended as potential enriching ingredients and fat substitutes in the development of new products in the functional food industry. © 2023 The Authors. Journal of The Science of Food and Agriculture published by John Wiley & Sons Ltd on behalf of Society of Chemical Industry.