Certain food by-products, including not-good-for-sale apples and pomegranate peels, are rich in bioactive molecules that can be collected and reused in food formulations. Their extracts, rich in pectin and antioxidant compounds, were obtained using hydrodynamic cavitation (HC), a green, efficient, and scalable extraction technique. The extracts were chemically and physically characterized and used in gluten-free and vegan cookie formulations to replace part of the flour and sugar to study whether they can mimic the role of these ingredients. The amount of flour + sugar removed and replaced with extracts was 5% and 10% of the total. Physical (dimensions, color, hardness, moisture content, water activity), chemical (total phenolic content, DPPH radical-scavenging activity), and sensory characteristics of cookie samples were studied. Cookies supplemented with the apple extract were endowed with similar or better characteristics compared to control cookies: high spread ratio, similar color, and similar sensory characteristics. In contrast, the pomegranate peel extract enriched the cookies in antioxidant molecules but significantly changed their physical and sensory characteristics: high hardness value, different color, and a bitter and astringent taste. HC emerged as a feasible technique to enable the biofortification of consumer products at a real scale with extracts from agri-food by-products.