The study investigates the interaction between the human epidermal growth receptor 2 (HER2) and amygdalin, a compound found in peaches, almonds, and apples. To assess the potential of amygdalin, the interaction between HER2 and amygdalin was explored using molecular docking and molecular dynamics simulations. Binding energies were evaluated for both the crystal and equilibrated HER2 structures. The effects of water on binding were also assessed. Molecular dynamics simulations analyzed structural changes in HER2, including interdomain distances, hydrogen bond fluctuations, dihedral angle shifts, and residue-residue distances at the dimerization arm. The free energy landscape was constructed to evaluate stability. Binding energies of −33.472 ​kJ/mol and −36.651 ± 0.867 ​kJ/mol were observed for the crystal and equilibrated HER2 structures, respectively, with water further enhancing binding to −41.212,4 ​± ​1.272,7 and −53.513 ± 1.452,3 ​kJ/mol. Molecular dynamics simulations revealed significant conformational changes in HER2, including a reduction in interdomain distance, fluctuations in hydrogen bond lengths, and a shift in dihedral angles from 60° to −30°. The residue-residue distance at the dimerization arm decreased, indicating conformational changes upon binding. The free energy landscape showed a deeper and more defined minimum in the bound state, reflecting enhanced stability. These findings highlight amygdalin’s potential as a therapeutic agent targeting HER2.