The nonfood waste of the sour cherry (Prunus cerasus L.) was used as an active material source in this study. After the active substance of the pomace was extracted by aqueous ethanol, the liquid extract was encapsulated in Arabic gum/maltodextrin (blend or alone) by spray-drying. The microencapsulation formulation was optimized by I-optimal design under combined design with two mixture components (Arabic gum and maltodextrin) and a numeric process factor (inlet temperature). The maximum yields (80.99%, 76.39%, 5.382 mg-TEAC/g-DM, and 0.722 mg-C3G/g-DM) of encapsulation efficiency (EE) in terms of total phenolic content, powder yield (PY), antioxidant activity, and total anthocyanin content (TAC) were achieved by ∼161 °C and Arabic gum alone (10%). Based on the analysis of the variance test, the interaction terms between the Arabic gum ratio and the inlet temperature were statistically significant (p < 0.05) for EE, while every single term was significant at p < 0.0001 in the case of PY. Regarding the antioxidant activity response, each term was significant at p < 0.05. Each term of the TAC analysis was generally statistically important at p < 0.0001. The microparticles were subjected to several morphological tests (particle size distribution, scanning electron microscopy, and diffuse reflectance infrared Fourier transform) and physicochemical measurements (moisture content, water activity, solubility, bulk density, tapped density, and Carr index). Finally, an in vitro digestion test was applied to obtain preliminary information on the developed microparticles before proceeding to the in vivo process.