This study examined Kefiran, an exopolysaccharide derived from milk kefir grains, as a novel biopolymer for encapsulating phenolic extracts from sunflower cake and its antimicrobial properties in the development of natural and functional food ingredients. Kefiran was obtained from kefir grains using three extraction protocols: hot water (M1), hot water with 30% trichloroacetic acid (M2), and mild heat combined with ultrasound at 60 °C (M3). The ultrasound-assisted method produced the highest carbohydrate concentration. Spectrophotometric assays (phenol–sulfuric and Bradford), Fourier transform infrared spectroscopy, scanning electron microscopy, thermogravimetric analysis, and water-holding capacity were employed to characterize the composition, structure, and morphology of the extracts, revealing well-preserved polysaccharide fingerprints and a highly porous microstructure, consistent with their potential application in food systems. Kefiran was then evaluated as an encapsulating agent in complex coacervation at pH 3.75, using three Kefiran-based wall formulations (M1, M2, and M3) with gum arabic and whey protein isolate (WPI) as co-wall materials, and their performance was compared with gum arabic and WPI controls. Across formulations, coacervate microcapsules achieved high encapsulation efficiencies (83–93%), tunable particle sizes, and predominantly negative zeta potentials, indicative of good colloidal stability. The Kefiran extract and coacervate microcapsules demonstrated significant antioxidant and antimicrobial activity against Staphylococcus aureus, Escherichia coli, Pseudomonas aeruginosa, and Candida albicans, with minimum inhibitory concentrations ranging from 250 to 1000 µg/mL. The findings support ultrasound-extracted Kefiran as a multifunctional biopolymer suitable for bioactive delivery and as a natural antimicrobial component in advanced functional food formulations.