Cancer survivors undergo meticulous examinations, including regular magnetic resonance imaging (MRI) scans, to monitor the risk of disease recurrence. The use of magnetic iron nanoparticles (MNPs) enhances MRI accuracy. However, post-injection, MNPs exhibit a notable affinity for binding with proteins and biomolecules, forming a dynamic protein coating called a protein corona (CORONA). While there are reports of its elimination in the liver and kidney metabolism system, patients undergoing this method have shown symptoms of liver problems and related enzyme alterations. This study aims to discern whether the impact of MNPs on liver enzymes significantly contributes to liver damage. The investigation focuses on the effects of magnetic nanoparticles (MNPs) on selected enzymes, including alanine aminotransferase (ALT), aspartate transaminase (AST), α-amylase, and lipase. Employing 104 experiments over a central composite design (CCD), the study evaluates the effects of agents on MNP and enzyme structure, stability, and properties: enzyme assay, electron microscopy, and circular dichroism of secondary structure after interaction with MNPs. The study’s findings unveil the intricate relationship between MNPs and liver enzymes, providing valuable insights for clinical practices and refining the safety profile of MRI. This comprehensive exploration contributes to our understanding of potential implications and aids in optimizing the use of MNPs in medical imaging for cancer survivors.