With the aim of improving the stability of penicillin G acylase (PGA), functional ionic liquids (ILs) were used to modify the surface chemistry of the supports on which they were physically adsorbed. Four kinds of ILs-specifically, 1-methyl-3-(triethoxysilylpropyl)-imidazolium salts, with Cl-, BF4-, PF6-, and Tf2N- as the anions (IL-Cl-, BF4-, PF6-, and Tf2N-, respectively)-were used to tune the hydrophilic or hydrophobic properties of the ILs. The synthesized ILs were first immobilized on magnetic silica nanoparticles (Fe3O4/SiO2), and the composite material (Fe3O4/SiO2-IL) was then applied to immobilize PGA via physical adsorption. The amount of protein loading, the specific activity, the immobilization yield, and the stability of immobilized PGA were investigated to evaluate the effects of the Its on the PGA immobilization. The results showed that PGA immobilized on Fe3O4/SiO2-ILs was more stable than that immobilized on Fe3O4/SiO2 with no IL modification. Among the four kinds of ILs tested, the hydrophilic ILs (IL-Cl-, and IL-BF4-) were superior to the hydrophobic ones (IL-PF6-, and IL-Tf2N-) for PGA immobilization. The reusability of the immobilized PGA on Fe3O4/SiO2-IL (BF4-) was evaluated; a high residual activity (70% of the initial activity) was observed after 9 consecutive operation cycles under the experimental conditions. This activity was 1.8 times higher than that of immobilized PGA on naked Fe3O4/SiO2 (40%).