Human milk oligosaccharides (HMOs) shape the developing infant gut microbiota. In this study, a semi-continuous colon simulator was used to evaluate the effect of 2 HMOs—2′-fucosyllactose (2′-FL) and 3-fucosyllactose (3-FL)—on the composition of infant faecal microbiota and microbial metabolites. The simulations were performed with and without a probioticBifidobacterium longumsubspeciesinfantisBi-26 (Bi-26) and compared with a control that lacked an additional carbon source. The treatments with HMOs decreased α-diversity and increasedBifidobacteriumspecies versus the control, but theBifidobacteriumspecies differed between simulations. The levels of acetic acid and the sum of all short-chain fatty acids (SCFAs) trended toward an increase with 2′-FL, as did lactic acid with 2′-FL and 3-FL, compared with control. A clear correlation was seen between the consumption of HMOs and the increase in SCFAs (−0.72) and SCFAs + lactic acid (−0.77), whereas the correlation between HMO consumption and higher total bifidobacterial numbers was moderate (−0.46). Bi-26 decreased propionic acid levels with 2′-FL. In conclusion, whereas infant faecal microbiota varied between infant donors, the addition of 2′-FL and 3-FL, alone or in combination, increased the relative abundance and numbersBifidobacteriumspecies in the semi-continuous colon simulation model, correlating with the production of microbial metabolites. These findings may suggest that HMOs and probiotics benefit the developing infant gut microbiota.