A substantial fraction of ingested polyphenols accumulate in the large intestine (LI), attached to undigested plant cell walls (PCW) (dietary fibre). Yet, whether these PCW-bound polyphenols alter the structure and function of the resident microbiota remains unclear. This study characterised bacterial populations during the in vitro fermentation of three standard polyphenols: ferulic acid (FER), (±)-catechin (CAT), and cyanidin-3-glucoside (CYAN), adsorbed individually or in combination to apple cell walls (ACW). During fermentation with porcine faeces, samples were collected at regular time-points (up to 72 hours) for bacterial 16S rRNA gene amplicon sequencing and fermentation end-product analyses (short-chain fatty acids and ammonium). The metabolic end-products differed to only a small extent between substrates, though significantly for propionate (P < 0.0001). Significant differences in microbial populations were noted between substrates tested (P < 0.0001). The presence of cyanidin-3-glucoside resulted in the most significant differences between bacterial communities during fermentation of the ACW substrate. Key microbes identified to be associated with the ACW with adsorbed polyphenols as well as individual polyphenols were: Phascolarctobacterium with ACW + FER and FER, the Lachnospiraceae family with ACW + CYAN, Parabacteroides with ACW + CYAN and CYAN, Collinsella and Coprococcus with ACW + CAT, and the Clostridiales order with ACW + CAT and CAT. This study has demonstrated the use of a simplified model to indicate any microbial effects of polyphenols associated with dietary fibre in whole fruits. This work has shown that individual polyphenols, or those adsorbed to PCW, have potentially very different effects on the gut bacteria. Future work could examine further polyphenols associated with a range of fresh fruits.