Apple pomace is a by-product of apple processing industries with low value and thus frequent disposal, although with valuable compounds. Acidified hot water extraction has been suggested as a clean, feasible, and easy approach for the recovery of polyphenols. This type of extraction allowed us to obtain 296 g of extract per kg of dry apple pomace, including 3.3 g of polyphenols and 281 g of carbohydrates. Ultrafiltration and solid-phase extraction using C18 cartridges of the hot water extract suggested that, in addition to the apple native polyphenols detected by ultra-high-pressure liquid chromatography coupled to a diode-array detector and mass spectrometry UHPLC-DAD-ESI-MSⁿ, polyphenols could also be present as complexes with carbohydrates. For the water-soluble polyphenols, antioxidant and anti-inflammatory effects were observed by inhibiting chemically generated hydroxyl radicals (OH•) and nitrogen monoxide radicals (NO•) produced in lipopolysaccharide-stimulated macrophages. The water-soluble polyphenols, when incorporated into yogurt formulations, were not affected by fermentation and improved the antioxidant properties of the final product. This in vitro research paves the way for agro-food industries to achieve more diversified and sustainable solutions towards their main by-products.