Functional beverages are increasingly used as a medium for targeted nutritional intervention, but liquid matrices present limitations that free bioactives frequently fail to overcome, such as precipitation, oxidation, and degradation during storage and gastrointestinal transit. This review explores the delivery systems that overcome these limitations in acidic, low-viscosity beverages, including biopolymer nanocarriers, solid-particle-stabilized (Pickering) emulsions, nanoemulsions, co-encapsulation systems and fermentation-derived exopolysaccharides. Beyond simple retention, we propose bioaccessibility (speciated) and sensory acceptability (clarity, mouthfeel, off-notes) as co-primary evaluation endpoints. The compatibility, stability, processing resilience (pasteurization, ultra-high temperature (UHT), high-pressure processing (HPP), pulsed electric field (PEF)), scalability and cost are combined in a comparative decision-support framework, and the sustainability assessment warns against assuming environmental benefits based on bio-based origin alone. Regulatory analysis compares the EU’s statutory nanomaterial framework with functional pathways in the US and UK, framing gastrointestinal dissolution screening as a pragmatic filter rather than a universal barrier. Lastly, we describe novel validation tools, gut-on-a-chip and organoid models combined with AI-powered multi-omics, not as replacements for human studies but as tools to accelerate formulation prioritization. The review proposes a matrix-aware framework for evaluating beverage delivery as a decision-governed translation problem that encompasses efficacy, acceptability, sustainability, and regulatory viability.