Scope Fucosylated human milk oligosaccharides (fHMOs) are metabolized by Bifidobacterium infantis and promote syntrophic interactions between microbiota that colonize the infant gut. The role of fHMO structure on syntrophic interactions and net microbiome function is not yet fully understood. Methods and results Metabolite production and microbial populations are tracked during mono‐ and co‐culture fermentations of 2ʹfucosyllactose (2ʹFL) and difucosyllactose (DFL) by two B. infantis strains and Eubacterium hallii . This is also conducted in an in vitro modeled microbiome supplemented by B. infantis and/or E. hallii . Metabolites are quantified by high performance liquid chromatography. Total B. infantis and E. hallii populations are quantified through qRT‐PCR and community composition through 16S amplicon sequencing. Differential metabolism of 2ʹFL and DFL by B. infantis strains gives rise to strain‐ and fHMO structure‐specific syntrophy with E. hallii . Within the modeled microbial community, fHMO structure does not strongly alter metabolite production in aggregate, potentially due to functional redundancy within the modeled community. In contrast, community composition is dependent on fHMO structure. Conclusion Whereas short chain fatty acid production is not significantly altered by the specific fHMO structure introduced to the modeled community, specific fHMO structure influences the composition of the gut microbiome.