Scope Next to galacto‐oligosaccharides (GOS), starch‐derived isomalto‐oligosaccharide preparation (IMO) and isomalto/malto‐polysaccharides (IMMP) could potentially be used as prebiotics in infant formulas. However, it remains largely unknown how the specific molecular structures of these non‐digestible carbohydrates (NDCs) impact fermentability and immune responses in infants. Methods and Results In vitro fermentation of GOS, IMO and IMMP using infant fecal inoculum of 2‐ and 8‐week‐old infants shows that only GOS and IMO are fermented by infant fecal microbiota. The degradation of GOS and IMO coincides with an increase in Bifidobacterium and production of acetate and lactate, which is more pronounced with GOS. Individual isomers with an (1↔1)‐linkage or di‐substituted reducing terminal glucose residue are more resistant to fermentation. GOS, IMO, and IMMP fermentation digesta attenuates cytokine profiles in immature dendritic cells (DCs), but the extent is dependent on the infants age and NDC structure. Conclusion The IMO preparation, containing reducing and non‐reducing isomers, shows similar fermentation patterns as GOS in fecal microbiota of 2‐week‐old infants. Knowledge obtained on the substrate specificities of infant fecal microbiota and the subsequent regulatory effects of GOS, IMO and IMMP on DC responses might contribute to the design of tailored NDC mixtures for infants of different age groups.