Metabolism of complex non-commercial fructans by Bifidobacteria has not been explored. In this work the production of the extracellular, cell-bound and intracellular β-fructofuranosidases by the probiotic Bifidobacterium longum subsp infantis ATCC 15697 in culture medium containing agave fructan and chicory inulin as carbon source was evaluated. The analysis of the profile of products formed in the hydrolysis of agave and inulin fructans by the three enzymatic fractions and the proteomic analysis of B. longum subsp infantis ATCC 15697 indicated the importance of B.longum_l1, an exo-β-fructofuranosidase, in the metabolism of the prebiotics studied. We found that B. longum hydrolyzes inulin and agave fructan through an exo-type mechanism involving B.longum_l1 exclusively and consumes low molecular weight fructans first in spite of their structure, suggesting that B. longum growth in these two structurally different substrates depends more on fructan molecular weight than on its chemical nature.