This study investigates Fructooligosaccharides (FOSs) production as prebiotics to promote gut health and overall well-being. Various production methods for FOSs were explored, leveraging novel engineered inulosucrase (IN) and levansucrase (LV) enzymes. The methodologies included batch stirred reactors with free enzymes and fixed-bed reactors utilizing enzymes immobilized on hydrogel chitosan beads (HGBs) and core-shell chitosan beads (CSBs). The study found that free enzymes exhibited the highest sucrose consumption rates, with IN achieving 142.8 g/L∙h and LV achieving 82.9 g/L∙h. However, CSB-immobilized enzymes demonstrated substantial enzyme savings (55% and 41% reduction in IN and LV consumption, respectively) through reuse across multiple cycles, while delivering superior FOSs yields. CSB-immobilized enzymes outperformed HGB-immobilized enzymes in terms of immobilization efficiency, activity recovery, sucrose conversion, FOSs yields, and repeatability. A novel reactor setup involving interconnected fixed-bed reactors with different enzymes in series produced promising results, generating novel FOSs species alongside expected I-FOSs and L-FOSs. Consumable cost analysis indicated that while free enzyme usage is initially cost-effective (5.09–7.06 USD/kg FOSs), significant increases in LV prices could make CSB immobilization a cost-competitive alternative. This study highlights the potential of innovative enzyme immobilization strategies and reactor designs for efficient FOSs production, considering both performance and economic feasibility.