The functionalization of food products with agri-industial residues is of great interest. Apple and beetroot pomace flour, abundant in dietary fiber and antioxidants, were incorporated into jelly candies using agar, pectin, or gelatin. Three functional formulations were devised for each flour type at the pilot scale, resulting in jelly candies with desirable sensory properties and texture. The high content of total polyphenolics, flavonoids, betacyanins, and betaxantines was determined upon in vitro digestion. The influence of different matrices on these bioactives, crucial for exerting antioxidant activity, was evaluated using DPPH and FRAP assays on both fresh and nine-month stored jelly candies, showcasing good bioavailability and retention. Enrichment with APF and BPF also led to reduced postprandial glucose levels, glycemic index, and load determined in vivo. These findings affirm that compositionally optimized innovative formulations of jelly candies facilitate the efficient delivery of compounds with anti-obesity effect from upcycled raw materials.