Phlorotannins (PHT) are phenolic substances found in marine brown seaweeds that have a lot of different biological effects. However, their poor stability restricted their usage in different fields. Here, we encapsulated PHT using a freeze-drying technique. Process parameters, including wall material type (maltodextrin, whey protein, and their combination), wall concentration (0.03–0.1 w/v), and core-to-wall ratio (2–5), were optimized using the response surface method with a central composite design (CCD) to attain the best capsule. The optimum encapsulation with the highest PHT efficiency (85.67%) and antioxidant activity (67.34%) was produced with a whey protein/maltodextrin blend encapsulating at 0.03 w/v and 5 PHT-to-wall ratios. Findings from SEM studies on optimal capsules revealed that the particles are irregular in shape, with some pores on the surface. Furthermore, the FTIR study validated the encapsulation of PHT, and the TGA data suggested that encapsulation enhanced the thermal stability of PHT. Further, encapsulated PHT (En-PHT) was added to pasteurized milk to increase its shelf life. The findings indicate that the addition of En-PHT restricts microbiological proliferation, prolonging milk’s shelf life from 4 days to 8 days while maintaining acceptable sensory attributes. This study suggests that En-PHT could be exploited as an ingredient to produce new, functional milk.