Polyphenols called procyanidins can be extracted from agro-industrial waste like litchi peel and coffee pulp. However, their efficacy is limited due to instability, which hinders both the bioavailability and preservation of their activity. This study aims to establish the ideal encapsulation conditions required to preserve the procyanidin properties found in extracts taken from litchi peel and coffee pulp. To attain the maximum procyanidin encapsulation efficacy (EE), the Taguchi method was utilized to streamline the spray-drying conditions for different wall materials-maltodextrin (MD), whey protein (WP), citrus pectin (CP), and skim milk (SM). The optimized conditions consisted of feed flow (3, 4.5, and 6 mL/min), temperature (125, 150, and 175 °C), and airflow (30, 35, and 40 m3/h). The microcapsules were characterized using ABTS, DPPH, lipoperoxidation, and scanning electron microscopy. Objective evaluations revealed that MD was the most effective encapsulation material for the litchi extract, whereas WP was the optimal option for the coffee extract. Of all the factors considered in the spray-drying process, feed flow had the strongest impact. The spray-drying process for the litchi peel extracts achieved high procyanidin encapsulation efficiencies at a feed flow rate of 4.5 mL/min, a temperature of 150 °C, and an airflow rate of 35 m3/h. Meanwhile, the coffee extract spray drying achieved similar results at a feed flow rate of 4.5 mL/min, a temperature of 175 °C, and an airflow rate of 40 m3/h. Encapsulation efficiencies of 98.1% and 93.6% were observed for the litchi and coffee extracts, respectively, under the mentioned optimal conditions. The microencapsulation process was successful in preserving the antioxidant properties of procyanidins. The microcapsules' size ranged from 2.6 to 3.2 micrometers. The results imply that the phenolic compounds present in the extracts function as effective antioxidant agents.