Pomegranate fruit is recognized as an important source of health compounds and its juicy arils represent the most commercially exploitable part of the fruit. Nevertheless, by-products coming from pomegranate juice processing represent both a challenging disposal problem and a promising source of health ingredients. In particular, the marcs obtained after juice squeezing are usually discarded or used for oil production in virtue of their lipophilic fraction, although the residues of pericarp and arils are proven to still be a good source of hydrophilic compounds such as polyphenols. Pulsed ultrasound-assisted extraction, using just water as solvent, and spray-drying microdispersion, using low methoxyl pectin as polymeric matrix, have been employed, respectively, to extract and formulate the water-soluble bioactive molecules from these by-products. From 100 g of pomegranate fresh marcs, almost the same quantity of phenolic compounds found in 100 mL of the corresponding juice can be extracted with similar antioxidant activity, but with higher content in vitamin C and practically without total soluble solids. The extracts have been sprayed obtaining powders with an encapsulation efficiency of about 50%. The extracts, both before and after the microparticles production, have been characterized and their capacity in inhibition of platelets aggregation induced by thrombin has been tested ex vivo on human platelets (% inhibition: about 60% and 30% before and after microencapsulation, respectively). Finally, fresh-cut apple wedges were enriched by vacuum impregnation with the formulated extracts, tentatively used as potential novel ingredients, obtaining “polyphenol-enriched” apples.