This study aimed to compare the nutritional, phytochemical, and sensory characteristics of wheat flour (WF) cookies enriched with different proportions of lupin sprout flour (LSF) and those with different proportions of lupin green sprout (LGS). To achieve this, a control cookie (CC); three cookies with 10%, 20%, and 30% of LSF, respectively, CLSF1, CLSF2, and CLSF3; and three other cookies (CLGS1, CLGS2, and CLGS3) with 10%, 20%, and 30%, respectively, were produced. The proximate composition of each cookie was analyzed using AOAC methods. Also, the measurements of the total polyphenol content, antioxidant activity, individual polyphenols, glycemic index, and a sensory analysis were carried out using recent and accurate methods. The contribution of the main nutrients from 100 g of product to the required daily dose was also calculated. Data analysis revealed that cookies with LSF were richer than cookies with LGS in protein, fat, and energy values. CLGS3 was 35.12%, 1.45%, and 5.0% lower in protein, fat, and energy content than CLSF3, respectively. On the other hand, CLSF3 was lower than CLGS3, with 48.2% and 12.4% in moisture and mineral substances, respectively. Both cookies were lower in carbohydrates than the CC (65.20 g/100 g). Still on the subject of micro- and macronutrients, cookies with LSF were richer than those with LGS in all the minerals analyzed. The study also revealed improvements in phytochemical properties, such as total and individual polyphenols and antioxidant activity with the percentage of lupin sprout flour addition. The sensory analysis revealed that, for LSF and LGS cookies, the 10% samples were the most appreciated by consumers, irrespective of the sensory attributes studied. The glycemic index of the CLSF2 product was lower compared to the CC. This study shows that the LSF cookies have better nutritional, phytochemical, and sensory values than the LGS cookies. LSF is, therefore, better suited than LGS to the enrichment of bakery products in general and cookies in particular. The paper provides significant information to estimate the contribution of the consumption of functional products based on lupin sprouts to the required daily dose of food nutrients and the impact on the glycemic index of fortified products.