Enzymatic/Spectrophotometric AOAC 999.03 fructan measurement method was modified with the objective to quantify agave fructans. Usefulness of the modified method was confirmed in pure agave fructans. Modified method result in about 25% of underestimation when fructans were mixed with food matrices. The effect over fructan losses resulted from thermal process was evaluated. Long chain fructans achieve better resistance in comparison with native fructans (8% of thermal loses) no matter the source of ingredient. In the case of native fructans, agave ingredients showed lower degradation in baked bread in comparison with chicory fructans.