A new in vitro fermentation model with immobilised infant faecal microbiota simulating the proximal colon of a formula-fed baby was developed and used to test the effects of known prebiotic fructans. Intestinal fermentation, based on a previously developed colonic fermentation model, using a new feeding medium simulating a formula-fed infant ileal chyme, was carried out for seventy-one consecutive days divided into four stabilisation periods intercalated with four prebiotic treatment periods. At the end of the first stabilisation period, total bacterial concentration in colonised beads and in faecal sample was similar, metabolite concentrations returned to stabilisation values after each treatment period. As expected, the four prebiotic treatments significantly increased the bifidobacterial populations, whereas they decreased bacteroides and clostridia. No difference was observed in the prebiotic effect of these substrates selected. The treatments significantly increased total production of SCFA and decreased ammonia compared to stabilisation periods. Long-term stability of the system together with the reproducibility of the known prebiotic effects highlights the potential of the present model to quantify and compare the effects of different substrates in a formula-fed infant microbiota within the same fermentation experiment.