Conventional treatments for peptic ulcer disease often suffer from reduced drug efficacy and bioavailability due to degradation by gastric acid and digestive enzymes. This study aims to develop a stable drug delivery carrier through the interfacial coacervation method to enhance drug stability within gastrointestinal delivery systems. Whey protein isolate (WPI) was first self-assembled into whey protein amyloid fibrils (WPI-AFs) under high-temperature and acidic conditions. Subsequently, hybrid capsules were synthesized via interfacial coacervation between WPI-AFs and hyaluronic acid (HA). Compared with conventional carriers, the hybrid capsules exhibited higher biocompatibility and minimized the risk of immune or toxic responses. Moreover, the hybrid capsules enabled stable and sustained drug release in the gastrointestinal tract, protecting bioactive drugs from degradation by gastric acid and enzymes. At this stage, the optimal conditions for amyloid fibrillogenesis of WPI have been successfully established, and the resulting fibrils were characterized using various biophysical, spectroscopic, and microscopic techniques. The WPI-AF/HA hybrid capsules were successfully fabricated, and their functional groups, surface charge, and microstructure were analyzed. Furthermore, the encapsulation efficiency (EE%) and loading capacity (LC%) of the bioactive drug riboflavin (RF) were determined, followed by in vitro drug release studies in simulated gastric fluid to investigate the release kinetics. Overall, this study successfully synthesized a novel type of drug-encapsulating carrier, and the resulting hybrid capsules present a promising platform for drug delivery in peptic ulcer therapy, potentially improving the safety and efficacy of clinical treatment.