Iron ions were implanted with a total fluence of 6 x 10^17 ions/m^2 into lithium niobate crystals by way of a sequential implantation at different energies of 95, 100 and 105 MeV respectively through an energy retarder Fe foil to get a uniform Fe doping of about few microns from the surface. The implanted crystals were then annealed in air in the range 200–400 °C for different durations to promote the crystalline quality that was damaged by implantation. In order to understand the basic phenomena underlying the implantation process, compositional in-depth profiles obtained by the secondary ion mass spectrometry were correlated to the structural properties of the implanted region measured by the high resolution X- ray diffraction depending on the process parameters. The optimised preparation conditions are outlined in order to recover the crystalline quality, essential for integrated photorefractive applications.