Ceramic and polymeric membrane systems were compared at the pilot scale for separating agave fructans into different molecular weight fractions that help to diversify them into more specific industrial applications. The effect of the transmembrane pressure of ultrafiltration performance was evaluated through hydraulic permeability, permeate flux and rejection coefficients, using the same operating conditions such as temperature, feed concentration and the molecular weight cut-off (MWCO) of membranes. The fouling phenomenon and the global yield of the process were evaluated in concentration mode. A size distribution analysis of agave fructans is presented and grouped by molecular weight in different fractions. Great differences were found between both systems, since rejection coefficients of 68.6% and 100% for fructans with degrees of polymerization (DP) > 10, 36.3% and 99.3% for fructooligosaccharides (FOS) and 21.4% and 34.2% for mono-disaccharides were obtained for ceramic and polymeric membrane systems, respectively. Thus, ceramic membranes are better for use in the fractionation process since they reached a purity of 42.2% of FOS with a yield of 40.1% in the permeate and 78.23% for fructans with DP > 10 and a yield of 70% in the retentate. Polymeric membranes make for an efficient fructan purification process, eliminating only mono-disaccharides, and reaching a 97.7% purity (considering both fructan fractions) with a yield of 64.3% in the retentate.