The combination of polyphenols and probiotics offers a promising strategy for developing multifunctional solutions in health and nutrition. Polyphenols, renowned for their antioxidant and anti-inflammatory properties, and probiotics, acknowledged for their capacity to modulate gut microbiota, exhibit a synergistic relationship that can enhance the effectiveness of both components. This synergy arises from the ability of probiotics to metabolize polyphenols into bioactive compounds with improved bioavailability, while polyphenols contribute to a gut environment conducive to probiotic survival, growth, and activity. However, the effective delivery of these bioactive compounds and viable probiotics to specific gastrointestinal (GI) tract regions remains a critical challenge, limiting the impact of nutraceuticals and functional foods on health outcomes. This study aimed to develop a robust co-delivery system integrating a probiotic strain and a bioactive polyphenol using the innovative vacuum facilitated diffusion (VFD) technique. VFD has been proposed as a novel encapsulation method with the potential to protect bioactive compounds against harsh GI conditions and reduce exposure to intense manufacturing processes. Moreover, VFD may enhance microbial traits that support probiotic activity throughout the GI tract. Despite its potential, the capabilities and limitations of VFD require thorough investigation to advance the co-delivery system toward application trials. The research focused on constructing a co-delivery model using lactic acid bacteria strains from the Lactobacillaceae family, incorporating catechin as the phenolic compound. The study explored how VFD influences microbial metabolism, aiming to enhance probiotic functionality. To facilitate this analysis, a protocol for nuclear magnetic resonance (NMR) sample preparation using microbial biofluids was developed, allowing a deeper understanding of the metabolic mechanisms triggered by VFD in microbial cells. The Lactobacillus rhamnosus GG (LGG) strain was chosen for its potential to improve survival in the GI tract. Experiments were conducted in a controlled environment using MRS media to assess metabolic and growth behavior variations. Despite the promising hypothesis, the microbial assays and NMR analysis did not demonstrate significant changes attributable to the VFD process. The anticipated enhancements in probiotic persistence and survivability in the GI tract were not observed, limiting insights into the mechanisms underpinning the LGG + catechin co-delivery system. Nevertheless, the assays identified the vacuum application during VFD, rather than the presence of catechin or ethanol, as the primary factor contributing to decreased microbial viability. These findings suggest that further optimization of the VFD parameters is crucial to minimizing cellular stress and enhance the efficacy of the co-delivery system. Future studies should focus on refining the VFD process, exploring alternative probiotic strains, and evaluating the co-delivery system in dynamic GI models. The integration of polyphenols and probiotics through advanced techniques like VFD holds significant potential for advancing personalized nutrition and addressing complex health challenges in a sustainable and effective manner.