Biopolymeric systems that co-encapsulate probiotics and bioactive compounds ensure timely delivery in the gastrointestinal tract. Cyanidin 3-sambubioside is the dominant anthocyanin in Natal plum (Carissa macrocarpa). This study aims at the co-encapsulation of Natal plum (Carissa macrocarpa) juice inoculated with Lactiplantibacillus plantarum 75 (Ltp. plantarum 75) by freeze-drying using pea protein isolate, maltodextrin, and psyllium mucilage and evaluating their release in vitro. An encapsulation efficiency of >85% was noted in lactic acid bacteria (LAB) survival and anthocyanin content. Freeze-drying produced pinkish-red powder, rich in polyphenols and LAB (>6 Log CFU mL−1) after 14 days of storage. Natal plum juice + maltodextrin + pea protein isolate + psyllium mucilage + Ltp. plantarum 75 (NMPeaPsyB) showed the highest LAB population (6.74 Log CFU mL−1) with a survival rate of 81.9%. After digestion, NMPeaPsyB and NMPeaPsy had the highest LAB survival (>50%) at 67.5% and 67.5 ± 0.75%, respectively, and the highest bioaccessibility of cyanidin 3-sambubioside in Natal plum juice than the other co-encapsulation with other biopolymers. NMPeaPsy and NMPeaPsyB showed phenolic stability in the gastric phase and controlled release in the intestinal simulated phase. The antioxidant activities had strong correlations with cyanidin 3-sambubioside. The results confirmed that microencapsulation is important for improving stability and allowing for the development of functional foods.