Amid the global drive to identify green, and sustainable materials and natural antioxidants to meet the demands for biodegradable packaging materials in terms of yield, qualification, and application, citrus peels emerge as abundant, inexpensive, and often overlooked green sources suitable for innovative food packaging. In this study, citrus flavonoids (CF) and citrus pectin (CP) were obtained through sequential extraction technology from citrus by-products, followed by preliminary purification and characterization. The findings revealed that CP is an acidic heteropolysaccharide rich in arabinose and galacturonic acid, with hesperidin being the predominant flavonoid constituent of CF. Subsequently, we encapsulated CF into a matrix comprising soy protein isolate (SPI) and CP, creating innovative active films. These films were thoroughly assessed for their antioxidant, antimicrobial, physicochemical, morphological, optical, barrier, and mechanical properties. The results indicated a significant enhancement in the mechanical strength, heat resistance, and barrier properties of the composite films upon the addition of CP and CF. Moreover, the CF-loaded composite films exhibited remarkable antioxidant properties and demonstrated inhibitory effects against both Escherichia coli and Staphylococcus aureus. Employing these antimicrobial edible films for post-harvest preservation of red-grapes and pork revealed their effectiveness in extending the shelf life of both. Particularly, SPI/CP-CF films showed exceptional potential in prolonging the shelf life of red-grapes and pork, attributed to their reduced water vapor permeability and oxygen permeability values, along with their active antioxidant and antibacterial attributes. In conclusion, these composite films exhibit significant promise as multifunctional active packaging materials for fruit and pork preservation. Additionally, considering that citrus peels are by-products generated during food processing, transforming these readily available waste resources into value-added materials represents an innovative and sustainable approach, contributing to eco-friendliness.