In this study an attempt has been made to investigate the effect of metal ion substitution on the structure and spectra of azurin using two-layer ONIOM (our own N-layered integrated molecular orbital + molecular mechanics) approach. It is evident from the results that the overall structure of the protein is not altered by metal ion substitution; nevertheless, the metal ion binding site undergoes noticeable changes. The present study highlights the importance of protein milieu in the prediction of structure, electronic, and spectral properties of native and substituted azurins and illustrates the usefulness of ONIOM approach in the designing and engineering of metalloproteins.