Insulin is a therapeutic peptide used as a remedy for diabetes. However, it must be administered daily because of its high clearance rate and poor bloodstream stability. Due to its biocompatibility and high encapsulation efficacy, chitosan and its derivatives attracted attention as a suitable candidate for protein delivery vehicles. Herein, the Insulin polypeptide structure and dynamics were investigated during the encapsulation in the polyacrylic acid / deoxycholic acid-modified chitosan copolymers. The fluorescence and far-UV circular dichroism (CD) spectroscopies data showed the structural stability of Insulin in the presence of the copolymer and the possibility of hydrophobic interaction occurrence during the complex formation. The molecular dynamics (MD) simulation data confirmed the role of hydrophobic residues of Insulin in the adsorption process and revealed information on the main driving forces in interaction initiation. The present study results promise new designs and applications for chitosan nanoparticle-based protein delivery systems.