This study investigated the effectiveness of immobilizing Saccharomyces cerevisiae invertase (SInv) on magnetite nanoparticles to produce fructooligosaccharides (FOSs). Based on the existing literature and accompanied by parameter estimation, a modified kinetic model was employed to represent the kinetics of sucrose hydrolysis and transfructosylation using SInv immobilized on magnetite nanoparticle surfaces. This model was utilized to simulate the performance of batch reactors for both free and immobilized enzymes. The maximum FOS concentration for the free enzyme was determined to be 123.1 mM, while the immobilized case achieved a slightly higher concentration of 125.4 mM. Furthermore, a continuous stirred-tank reactor (CSTR) model was developed for the immobilized enzyme, resulting in a maximum FOS concentration of 73.96 mM at the reactor’s outlet and a dilution rate of 14.2 h−1. To examine the impact of glucose inhibition on FOS production, a glucose oxidase reaction mechanism was integrated into the fitted immobilized theoretical model. In a batch reactor, the reduction or elimination of glucose in the reactive media led to a 2.1% increase in FOS production. Immobilizing the biocatalyst enhanced the overall performance of SInv. This enzyme immobilization approach also holds the potential for coupling glucose oxidase onto functionalized nanoparticles to minimize glucose inhibition, thereby improving FOS synthesis and facilitating optimal enzyme recovery and reuse.