AbstractThis study deals with the effect of Cu on hydroxyapatite (HAp) thin films on silicon substrates prepared by pulsed laser deposition (PLD) technique for Cu concentrations ranging from 0 to 0.8 wt.%. Fourier transform infrared spectroscopy and Raman spectroscopy provide additional evidence of HAp in the films, which exhibit characteristic HAp bands such as the 960 cm−1 phosphate ion band. The X‐ray diffraction patterns confirm the presence of HAp, without copper‐related peaks, suggesting that it is not incorporated into the HAp lattice, which is present as an amorphous phase. X‐ray photoelectron spectroscopy confirms the presence of Cu on the HAp thin films, possibly related to the adsorption of Cu2+ on HAp surfaces through electrostatic or interactions with (PO4)3− groups. Atomic force microscopy shows that the roughness of the films varies depending on the presence or absence of copper ions. Finally, density functional theory and kinetic Monte Carlo simulations explain the effects of atomic diffusion on roughness and HAp clustering. These changes correlate with the contact angle values, indicating the formation of hydrophobic films due to copper inclusions.