In this study, we prepared various anionic magnetic adsorbents through the carboxyl functionalization of core/shell-structured Fe3O4/SiO2 (FS) particles by either succinic anhydride (FSC), low-molecular-weight (MW 1800) polyacrylic acid (PAA) (FSP1), or high-molecular-weight (MW 100,000) PAA (FSP2), and then, investigated the effect of the structure of adsorbents and operational parameters on their performance for the lysozyme separation. The type and size of functional molecules have significant effects on the surface concentration of functional carboxyl groups onto the adsorbent particles (increase in the order of FSP2 > FSP1 > FSC), and consequently on the adsorption efficiency (AE) (∼100, 98, and 62%, respectively) and adsorption capacity (AC) (∼1000, 980, and 621 mg·g-1, respectively) of the adsorbents. However, the loss of the antibacterial activity of separated lysozyme molecules due to the molecular conformational change increased in the order of FSP2 > FSP1 = FSC, as compared to the free lysozyme. The application of basic buffer solutions for the elution of adsorbed enzyme molecules resulted in more adverse effects on the enzyme activity. The obtained results recommend that FSP1 can be used as a suitable anionic adsorbent for the isolation of positively charged proteins, owing to its high adsorption capacity, excellent reusability, and structural stability, as well as the high purity, structural stability, and activity recovery of the isolated proteins.