Purpose: The aim of this work was to prove the synergic complementarity of attenuated total reflection Fourier transform infrared microspectroscopy (micro-ATR FTIR), scanning electron microscopy (SEM) coupled with energy-dispersive x-ray spectroscopy (EDS), and x-ray microcomputed tomography (micro-CT) by studying implant samples with bone affected by peri-implantitis. Materials and Methods: Six samples of implanted bone affected by peri-implantitis and one control healthy bone were analyzed. Thick bone sections included in epoxy-resin and removed implants were analyzed by micro-ATR FTIR, SEM-EDS, and micro-CT. Results: Micro-ATR FTIR revealed the complex nature of the bone composition. Vibrational bands characteristic of both mineral bone phase (acidic phosphates, CO₃^2- groups) and organic bone phase (mostly collagen) could be recognized, and their proportion could be seen to change accordingly with the bone degradation. Similarly, SEM-EDS clearly revealed the cortical nature of the control mandible and its homogenous mineral composition. On the contrary, EDS analyses performed over relevant portions of pathologic samples revealed that defective areas were almost Ca and P free. Micro-CT data showed that the morphology of the interface was smooth and linear in the physiologic peri-implant bone, while in the pathologic samples, an altered morphology was evident. Conclusion: This study demonstrated that morphologic, elemental, and biochemical modifications of peri-implant bone can be studied using micro-ATR FTIR, SEM-EDS, and micro- CT. The complement of these techniques can be considered a new multipurpose approach to investigate bone affected by peri-implantitis. Keywords: bone-implant interactions, CT imaging, surface chemistry