This work investigated the fructooligosaccharides (FOS) synthesis by immobilized inulinase obtained from Kluyveromyces marxianus NRRL Y-7571 in aqueous and aqueous-organic systems using sucrose as substrate. The sequential strategy of experimental design was used to optimize the FOS conversion in both systems. For the aqueous-organic system, a 2(6-2) fractional design was carried out to evaluate the effects of temperature, sucrose concentration, pH, aqueous/organic ratio, enzyme activity, and polyethylene glycol concentration. For the aqueous system, a central composite design for the enzyme activity and the sucrose concentration was carried out. The highest fructooligosaccharides yield (Y FOS) for the aqueous-organic system was 18.2 ± S0.9 wt%, at 40 ºC, pH 5.0, sucrose concentration of 60% (w/w), enzyme activity of 4 U.mL-1, and aqueous/organic ratio of 25/75 wt%. The highest Y FOS for the aqueous system was 14.6 ± 0.9 wt% at 40 ºC, pH 5.0, sucrose concentration of 60 wt%, and enzyme activity of 4.0 U.mL-1.