This study focused on the effects of candidate prebiotics polydextrose (PDX) and xylitol on the microbial community and its metabolic activity in a colon simulator. A semicontinuous, anaerobic culture system was used with 4 vessels mimicking the conditions in the human large intestine from proximal to distal colon. Bacterial inocula for the independent simulations were obtained from fecal samples of different donors. Synthetic medium, mimicking the contents of the small intestine, containing either 2% of the prebiotic candidate or no added carbohydrates as a control, was fed to the system. After 48 h of simulation samples were collected and analyzed. A sustained degradation of polydextrose throughout the colon model and a more rapid degradation of xylitol were observed. The fermentation of both compounds was characterized by a significantly increased production of short-chain fatty acids (SCFA). Polydextrose increased the concentrations of all SCFA, especially acetate and propionate, and xylitol especially the concentration of butyrate. Branched-chain fatty acids (BCFA) levels decreased significantly as a result of polydextrose and xylitol supplementation, whereas biogenic amine levels remained mostly unchanged. Thus, a beneficial shift in the metabolic patterns of the colon microbes was measured with both of the tested products. These in vitro studies provide evidence to the prebiotic characteristics of polydextrose; also, further beneficial properties of xylitol were demonstrated in the colon model.