<p>The work was devoted to a study of the structural and functional properties of the cysteine proteases bromelain, ficin, and papain immobilized on the stimulus-sensitive carrier poly(<i>N</i>,<i>N</i>-dimethylaminoethyl methacrylate). Immobilization of papain and bromelain on poly(<i>N</i>,<i>N</i>-dimethylaminoethyl methacrylate) was shown to lead to an increase in their catalytic activity by 1.6 and 1.2 times, respectively, while ficin activity decreased by ~40%. Molecular docking and IR spectroscopy made it possible to show the role of hydrophobic interactions and the formation of salt bridges in the formation of enzyme–polymer complexes. The results confirmed that the use of drugs based on cysteine proteases immobilized on poly(<i>N</i>,<i>N</i>-dimethylaminoethyl methacrylate) in segments of the chemical and pharmaceutical industries will increase the efficiency of existing compositions based on them.</p>