Recovering the bioactive components from pomegranate peel (PP) in the fruit-processing industry has attracted great attention in terms of minimizing the waste burden, as well as providing a new source of a multitude of functional compounds. The present study aimed to develop a feasible microencapsulation process of PP extract by using pectin and a pectin/2-hydroxypropyl-β-cyclodextrin (HP-β-CD) blend as coating materials. Microsized powders obtained by a spray drying technique were examined in terms of technological characteristics, exhibiting high powder yield and desirable moisture content, flowability, and cohesive properties. Assuming that the interactions with the used biopolymers occur on the surface hydrophobic domain, their presence significantly improved the thermal stability of the microencapsulated powders up to 200 °C. The health-promoting effects of PP have been associated with its high content in ellagitannins, particularly punicalagin. The obtained PP powders exhibited strong antioxidant and hypoglycemic potential, while an antimicrobial assay revealed their potent activity against Gram-positive bacteria. Additionally, an in vitro release study suggested that the used biopolymers can modify the release of target bioactive compounds, thus establishing a basis for developing an oral-controlled release system. Altogether, biowaste valorization from PP by the production of effective multifunctional microsized powders represents a sustainable way to obtain novel nutraceuticals and/or pharmaceuticals.