The development of plant-based functional beverages is often limited by inherent matrix defects, particularly undesirable off-flavors, astringency, and colloidal instability. Water kefir (WK), a highly resilient multispecies symbiotic consortium, offers a robust biorefining platform to address these challenges. This review systematically elucidates the underlying micro-ecological logic and biochemical mechanisms of WK-mediated plant matrix remodeling. We first detail how spatial niche differentiation and cross-feeding networks among lactic acid bacteria, yeasts, and acetic acid bacteria drive ecological homeostasis. Next, we highlight core molecular events that elevate sensory quality: protein unfolding for off-flavor elimination, enzymatic depolymerization of phenolics to mitigate astringency, and exopolysaccharide synthesis for rheological and flavor diffusion control. Finally, to overcome industrial scale-up challenges, we outline a precision fermentation framework, integrating systems multi-omics, real-time biomimetic monitoring, and sensory topological modeling. Ultimately, this synthesis provides theoretical guidance for the reverse flavor engineering and targeted nutritional design of novel plant-based beverages.