Cytochrome c (Cyt-c) is a heme-containing protein that plays a vital role as an electron carrier in the mitochondrial respiratory chain. Cyt-c possesses peroxidase-like activity in the native state despite its six-coordinated heme iron. In this work, we studied the effect of magnetic ionic liquids (MILs) on the peroxidase activity of Cyt-c. Guaiacol oxidation was used to probe the activity of Cyt-c in the presence of cholinium (Ch)-based MILs such as [Ch][FeCl4] and [Ch]2[MnCl4]. A detailed kinetics and thermodynamics study on the activity of Cyt-c in the presence of MILs was investigated with the help of isothermal titration calorimetry (ITC), UV–vis, circular dichroism (CD), and fluorescence spectroscopy. The peroxidase activity of Cyt-c increases by twofold in the presence of [Ch][FeCl4] and only 20% in the presence of [Ch]2[MnCl4] IL. This correlates with the accessibility of the heme iron of Cyt-c. Molecular docking and molecular dynamic simulations were also employed to explore the mechanism of the interaction. The increase in the peroxidase activity of Cyt-c is attributed to the perturbation in the native sixth coordination bond of methionine-80 associated with the heme region of Cyt-c. Since not much work has been done on the enzymatic activity in the presence of MILs, we hope this will set the platform to use MILs to modulate and control enzymatic activity and catalysis.