The aim of the research was to develop microencapsulated powders of bilberry and chokeberry extracts via the spray drying technique. Two biopolymers, pectin alone and in combination with HP-β-CD, were used to preserve the antioxidant, hypoglycemic, photoprotective, and antimicrobial bioactivity of the berry leaf extracts. Moreover, the formed powders were characterized in terms of technological, chemical, and several biological properties. The obtained micro-sized powders (mean average particle diameter from 3.83 to 5.94 µm) demonstrated a process yield of up to 73%. The added biopolymers improved the flowability and cohesive properties of the powders and increased their thermal stability to 170 °C. The total content of polyphenolics in the powders ranged from 323.35 to 367.76 mg GAE/g DW for bilberry and from 186.85 to 227.59 mg GAE/g DW for chokeberry powders; meanwhile, chlorogenic acid was the predominant compound in powders. All samples showed stronger α-glucosidase inhibitory activity (IC50 values ranged from 5.00 to 19.59 µg/mL) compared with the reference standard. The study confirmed that spray drying is a suitable method for the preservation of the polyphenolic-rich extracts, while the addition of carriers has a positive effect on the improvement of microencapsulated powders’ properties.