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The objective of the current study was to evaluate the potential of 2′-FL and GOS, individually and combined, in beneficially modulating the microbial composition of infant and toddler (12–18 months) feces using the micro-Matrix bioreactor. In addition, the impacts of GOS and 2′-FL, individually and combined, on the outgrowth of fecal bifidobacteria at (sub)species level was investigated using the baby M-SHIME^® model. For young toddlers, significant increases in the genera <i>Bifidobacterium</i>, <i>Veillonella</i>, and <i>Streptococcus</i>, and decreases in <i>Enterobacteriaceae</i>, <i>Clostridium</i> XIVa, and <i>Roseburia</i> were observed in all supplemented fermentations. In addition, GOS, and combinations of GOS and 2′-FL, increased <i>Collinsella</i> and decreased <i>Salmonella</i>, whereas 2′-FL, and combined GOS and 2′-FL, decreased <i>Dorea</i>. Alpha diversity increased significantly in infants with GOS and/or 2′-FL, as well as the relative abundances of the genera <i>Veillonella</i> and <i>Akkermansia</i> with 2′-FL, and <i>Lactobacillus</i> with GOS. Combinations of GOS and 2′-FL significantly stimulated <i>Veillonella</i>, <i>Lactobacillus</i>, <i>Bifidobacterium</i>, and <i>Streptococcus</i>. In all supplemented fermentations, Proteobacteria decreased, with the most profound decreases accomplished by the combination of GOS and 2′-FL. When zooming in on the different (sub)species of <i>Bifidobacterium</i>, GOS and 2’-FL were shown to be complementary in stimulating breast-fed infant-associated subspecies of <i>Bifidobacterium longum</i> in a dose-dependent manner: GOS stimulated <i>Bifidobacterium longum</i> subsp. <i>longum</i>, whereas 2′-FL supported outgrowth of <i>Bifidobacterium longum</i> subsp. <i>infantis</i>.