With the aim to overcome the limitations of hydrogel chitosan beads (HGBs), various types of chitosan, core–shell chitosan beads (CSBs), and dried chitosan beads (DBs) were synthesized. Physical and chemical properties were compared with those of HGBs. CSBs were proved to be an effective support because they displayed higher stability and capacity over the HGBs, and thus, were selected for enzyme immobilization. Recombinant inulosucrase (INU) from Lactobacillus reuteri 121 was immobilized on CSBs using glutaraldehyde as a cross-linker. Immobilized biocatalysts (INU-CSBs) were then used for the synthesis of inulin-type fructooligosaccharide (IFOS). Biochemical characterization revealed that the optimum pH of both INU-CSBs and free enzyme was unaltered at 5.5 whereas the optimum temperature of INU-CSBs shifted from 50 °C to 60 °C. Moreover, pH stability and thermostability of INU-CSBs significantly improved. For batch synthesis of IFOS, INU-CSBs retained approximately 45% of their initial catalytic activity after being reused for 12 cycles. IFOS was also continuously synthesized in a fixed-bed bioreactor for a reaction duration of at least 30 h. The high efficiency of INU-CSBs makes them very attractive for industrial applications.