The use of natural bioactive compounds in edible coatings provides a sustainable approach to reducing food spoilage and meeting consumer demand for safer food preservation. In this study, bioactive extracts from Brassica juncea (green mustard, GM) and Raphanus sativus (radish tango, RT) sprouts were encapsulated into zein/chitosan (Z/CH) microparticles (MPs) using a complex coacervation–based encapsulation approach. The encapsulated microparticles (MPs), characterized by FTIR and UV-Vis spectroscopy, demonstrated a high loading efficiency of up to 90% and maintained their antioxidant activity for up to 168 h. TGA and SEM tests confirmed that the edible films produced by incorporating these microparticles (MPs) into polyvinyl alcohol (PVA) and chitosan (CH) matrices had a more uniform microstructure and enhanced heat stability. The Z/CH/RT6:PVA (1:2) and Z/CH/GM6:CH (1:1) formulations of the films showed significant antioxidant and antibacterial action, with up to 22.4% DPPH inhibition and a 1-log decrease in Salmonella enterica CFU, respectively. Overall, the results underscore the promise of sprout-derived microparticles as components for developing active, biodegradable packaging films with improved functional properties.