The main conditions affecting the downstream process for purification of inulinase from Kluyveromyces marxianus var. bulgaricus ATCC 16045 were investigated. Parameters including the elution mode, linear rate, ionic strength, and elution pH were evaluated in order to achieve the best purification factor and recovery. The best purification factor and recovery were achieved in run 6 using a gradient elution mode with concentrations of NaCl ranging from 0 to 1 M, a linear flow rate of 100 cm/h and a pH value of 4.1. Under these conditions, the recovery was ~ 67.5% and the purification factor ~ 6.6-fold.