This work aimed to propose the reuse of processing waste from the Sicilian almond ( Batsch.) cultivar Tuono for the formulation of a new functional baked product (muffin) that is gluten- and lactose-free. Muffins were prepared using orange juice, rice flour, extra virgin olive oil, and enriched almond skin (3% and 6% /). The chemical-physical parameters, total phenols, and flavonoids (TPC and TFC), as well as the biological properties of the ingredients and muffins, were evaluated. Sensory analyses were also conducted. DPPH, ABTS, β-carotene bleaching, and FRAP tests were applied to measure the antioxidant potential. Muffin extracts were also tested against α-amylase and α-glucosidase enzymes. Muffins enriched with 6% almond skin (M6) showed the highest TPC and TFC with values of 26.96 mg gallic acid equivalent (GAE)/g and 24.12 mg quercetin equivalent (QE)/g, respectively. M6 exerted a promising antioxidant activity as an inhibitor of lipid peroxidation, with an IC of 15.44 μg/mL at 30 min incubation. Moreover, muffin M6 showed a promising α-glucosidase inhibitory effect (IC of 51.82 μg/mL). Based on the obtained results and supported by sensory analysis, muffins enriched with almond skin should be proposed as a promising example of upcycling for the development of a new functional bakery product.