The synthesis of nanoparticles using ionic liquids (ILs) has attracted intensive research; however, synthesis and surface tailoring of gold nanoparticles (AuNPs) using ILs for enzyme immobilization have not yet been reported. Herein, we synthesized the various IL-modified AuNPs using different ILs, which are having common cation 1-ethyl-3-methyl-imidazolium (EMIM) and variable anions [BF 4−1 (AuNP-IL1), (CH 3 OSO 3 ) −1 (AuNP-IL2), (CH 3 CH 2 OSO 3 ) −1 (AuNP-IL3), and Cl −1 (AuNP-IL4)] by reduction of gold salt. The formation of IL modified AuNPs has been confirmed using UV−vis, zeta-potential, FTIR, and transmission electron microscopy (TEM). Thereafter, the centrifuged IL-modified AuNPs are being immobilized with a lysozyme (Lyz) enzyme to evaluate the effect of different AuNP covering groups (capping agent and IL's anions) for Lyz microbial activity, thermal and structural stabilities through interaction studies, spectroscopic techniques, and morphology investigation by TEM. AuNP-IL1 has increased the microbial activity of Lyz up to 2.6 fold at the concentration of 4 nM, and AuNP-IL2 is highly efficient to dextrously preserve enzyme activity against packaging for 4 weeks. The higher Michaelis−Menten constant (K M ) has been observed for Lyz immobilized in the AuNP-IL2 due to higher binding with the AuNP-IL2. Apparently, the higher specific constant (K cat /K M ) of immobilized Lyz has been observed in the case of AuNP-IL3 and shows more specific binding of Lyz with this particular IL-mediated AuNPs. The significant thermal stability enhancement about 8.11 °C is observed for transition temperature (T m ) of Lyz in the presence of sulfur group-containing IL-modified AuNPs like AuNP-IL2 and AuNP-IL3, which depends on the specific interacting ability of these AuNPs with Lyz. Therefore, the study reveals the variant character of sulfur-containing IL-modified AuNPs for higher activity and thermal and structural stability of Lyz. Surprisingly, this has created a way to monitor sulfur and hydrophobic interactions on AuNPs for enzyme immobilization through means of controlling surface modifications and interactions.