Cocoa (Theobroma cacao L.) is an important source of bioactive compounds with high antioxidant capacity and antimicrobial properties. However, these compounds are susceptible to degradation by light, oxygen, pH, and temperature, which limits their functionality. This study evaluated the microencapsulation of CCN-51 cocoa extracts by spray drying, using maltodextrin (MD) and gum arabic (GA) as encapsulating agents, with the aim of preserving their bioactive activity and promoting their application in food. Microcapsules formulated with 5%GA showed the highest encapsulation efficiency (77.5%) and the highest phenolic content (92.7 GAE/g), showing significant differences compared to formulations with MD (p < 0.0001). Antioxidant capacity, quantified using the ABTS method, reached 583.3 µmol TE/g for 5% GA, significantly exceeding that of microcapsules with 10%MD (230.9 µmol TE/g; p < 0.0001). In terms of antimicrobial activity, microcapsules containing 5%MD showed greater inhibition against Escherichia coli (22.1 mm) and Staphylococcus aureus (12.3 mm), while those containing GA recorded halos of 10.1 mm and 12.1 mm. When applied to chicken muscle, treatments with 5%GA significantly reduced microbial growth for 72 h, demonstrating that the prepared microcapsules have high bioactivity, stability, and antimicrobial capacity in samples of meat products that are widely consumed and potentially susceptible to spoilage due to microbial growth.