Probiotic–Prebiotic Co-Encapsulation in Functional Dairy Foods: Current Technologies and Prospects for Integration with Milk-Derived Bioactive Peptides

Co-encapsulating probiotics with prebiotic substrates (PRO–PRE) is widely proposed as a route to functional dairy products, yet the terminology and the supporting evidence are applied inconsistently. This structured narrative review examines PRO–PRE co-encapsulation in dairy matrices and, as a complementary field, the encapsulation of milk-derived bioactive peptides. Scopus, Web of Science Core Collection, and PubMed were searched for publications from 1 January 2015 to 1 September 2026. Of 663 records retrieved, 420 remained after deduplication and 330 after screening; 117 were prioritized for technological assessment. Protection is consistent but partial: encapsulated Lacticaseibacillus rhamnosus in ice cream declined by 0.61 log CFU/g over 50 days of frozen storage, compared with 0.97 log CFU/g for free cells. Adding a substrate is not invariably beneficial, since sweet-whey–inulin microcapsules in Greek-style yogurt and inulin in ultrafiltered white cheese conferred no advantage over the carrier alone. Outcomes depend on strain, carrier, encapsulation method, and dairy matrix, and no method proved superior on every criterion. Physical co-localization was frequently reported as synbiotic function without evidence of selective substrate utilization. No validated dairy system combining a probiotic, a confirmed prebiotic, and a characterized milk-derived peptide was identified, and clinical validation is still lacking.