The aim of this study was to evaluate the effects of soy-based beverages manufactured with water-soluble soy extract, containing probiotic strains (Lactobacillus acidophilus LA-5 and Bifidobacterium longum BB-46) and/or acerola by-product (ABP) on pooled faecal microbiota obtained from lean and obese donors. Four fermented soy beverages (FSs) ("placebo" (FS-Pla), probiotic (FS-Pro), prebiotic (FS-Pre), and synbiotic (FS-Syn)) were subjected to in vitro digestion, followed by inoculation in the TIM-2 system, a dynamic in vitro model that mimics the conditions of the human colon. Short- and branched-chain fatty acids (SCFA and BCFA) and microbiota composition were determined. Upon colonic fermentation in the presence of the different FSs formulations, acetic and lactic acid production was higher than the control treatment for faecal microbiota from lean individuals (FMLI). Additionally, SCFA production by the FMLI was higher than for the faecal microbiota from obese individuals (FMOI). Bifidobacterium spp. and Lactobacillus spp. populations increased during simulated colonic fermentation in the presence of FS-Syn in the FMLI and FMOI. FS formulations also changed the composition of the FMOI, resulting in a profile more similar to the FMLI. The changes in the composition and the increase in SCFA production observed for the FMLI and FMOI during these in vitro fermentations suggest a potential modulation effect of these microbiotas by the consumption of functional FSs.