The present study was designed to analyze the advantages and limitations of using choline chloride:urea (ChCl:U) deep eutectic solvent (DES) as a cosolvent for versatile peroxidase (VP). The VP activity declined in the presence of increasing concentrations of ChCl:U. However, in the presence of ChCl:U, improved Km values were obtained for VP at pH = 7, in which the enzyme was nearly inactive in the absence of ChCl:U. Besides, the presence of ChCl:U caused higher exposure of hydrophobic clusters, formation of VP assemblies, and adoption of a more compact structure, as revealed by various fluorescence studies. Further studies using UV–Vis spectroscopy indicated that ChCl:U could protect VP from thermal denaturation and induce reorientation in the vicinity of heme. Moreover, far UV circular dichroism studies showed considerable changes in secondary structure elements of VP as an elevated α-helices content. Additionally, near UV circular dichroism spectroscopy demonstrated that the tertiary structure of VP was subjected to alteration when incubated in the presence of ChCl:U and confirmed the results of UV–Vis studies on probable reorganization of amino acids in the vicinity of heme.