A commercially available endo-inulinase from A. niger was successfully immobilized onto a chitin carrier. The optimum pH of endo-inulinase from A. niger was shifted by 1 unit higher after immobilization. The immobilized preparation was more stable at higher temperature than free enzyme, opening possibilities to operate continuously at 60 °C for a long period. Also, with immobilized endo-inulinase the bioconversion rate was high, which would be an advantage to prevent microbial contamination. A better distribution of the oligosaccharides (DP7–4) was obtained by applying a packed-bed column reactor and Jerusalem artichoke juice as substrate. Furthermore, from the technological standpoint, the system containing immobilized endo-inulinase was exploited for the continuous production of oligofructose from Jerusalem artichoke juice.