The global beverage market is rapidly evolving toward functional products fortified with bioactive ingredients like probiotics, polyphenols, vitamins, and omega-3 fatty acids. However, the inherent instability of these ingredients during processing, storage, and gastrointestinal transit compromises their efficacy and product viability. To address these challenges, micro- and nanoencapsulation have emerged as powerful technological solutions. This review provides a comprehensive and critical analysis of recent advances in micro- and nanoencapsulation strategies for fortifying dairy and non-dairy beverages. It focuses on emerging delivery systems, including hydrogel beads, polymeric complexes, emulsions, and bilayer vesicular systems, and evaluates their role in improving the stability, viability, and bioaccessibility of bioactive ingredients. The impact of these strategies on beverage quality, sensory profile, and commercial potential is also assessed. Numerous studies demonstrated that encapsulation can enhance the performance of functional ingredients across diverse beverage matrices, from dairy to plant-based alternatives. Specifically, tailored systems (e.g., coated particles, emulsion-gels, Pickering emulsions) improve probiotic survivability, shield antioxidants from degradation, and mask undesirable flavors, thereby improving the beverage's sensory attributes. Crucially, these technologies facilitate targeted release in the gut, enhancing bioaccessibility and the potential for bioavailability to maximize intended health benefits. Despite promising laboratory results, commercial adoption faces challenges in scalability, cost-effectiveness, and sensory impact. Long-term stability in complex beverage systems and the regulatory landscape for novel materials, particularly nanocapsules, requires further attention. This review underscores the transformative potential of encapsulation for creating advanced, health-promoting beverages while outlining the critical path for successful market translation from research to market.