Starch, dietary fibre, and polyphenols are key components of plant-based foods whose coexistence in carbohydrate-rich matrices defines both food structure and nutrition. While increasing attention has been given to pairwise interactions among these components, their combined (three-way) interactions remain poorly understood and are rarely captured in real food systems or clinical studies. Understanding pairwise, and particularly three-way, interactions require carefully designed and representative study models. This is especially challenging for plant cell wall materials, which must capture their chemical and supramolecular complexity, and for phenolic compounds, which should reflect their structural diversity and glycosylation patterns. To address this, we developed a model system in which component composition, structure, and concentration were tightly controlled. The model encompassed wheat starch, a bacterial cellulose analogue of the apple cell wall (aACW), and an apple pomace polyphenol extract, ensuring integrated chemically complex cell wall polysaccharides and a real mixture of apple polyphenols, predominantly glycosylated, assembled into supramolecular structures that mimicked the native deposition of cellulose within the polysaccharide matrix of plant cell walls (Figure 1). Blends - starch + polyphenols (S-PP), starch + aACW (S-aACW), starch + aACW + polyphenols (S-aACW-PP), and starch + polyphenol-preloaded aACW [S-(aACW:PP)] – ensuring consistent starch-aACW-polyphenol ratios were subjected to simulated hydrothermal processing (RVA), storage, and in vitro digestion using the INFOGEST model with pooled human saliva. Gut microbial responses were tested using in vitro fecal microbiota batch fermentations. The presence of polyphenols in both starch and S-aACW lowered pH and significantly reduced granular swelling and increased breakdown upon heating. These reductions in granular swelling were mitigated when polyphenols were pre-loaded within aACW, while their aACW-entrapment had no effect on breakdown, setback (short-term retrogradation), or water mobility. During storage, the inclusion of polyphenols or aACW increased the enthalpy of retrograded amylopectin, an effect intensified by combining free polyphenols and aACW (S-aACW-PP) but not when polyphenols were pre-loaded within aACW [S-(aACW:PP)]. aACW and polyphenols individually reduced starch digestibility. Notably, this effect at the end of the intestinal phase persisted only with free polyphenols, not with those pre-bound to aACW. Remarkably, beta-diversity analyses revealed strong clustering by treatment (including S-aACW-PP and S-(aACW:PP) despite their compositional similarity), underscoring the role of aACW-polyphenol interactions in modulating dietary fiber's prebiotic effect in starchy systems. These results demonstrate that the properties and bioactivities of starch, dietary fibers and phenolic compounds are interdependent in products containing them, such as whole grain products and formulated plant-based foods products fortified with phenolics and fibers. Results may therefore contribute to enhance the design, formulation and production of food products for health, beyond simply the content in bioactive nutrient and towards actual functionality.