MXenes are a young family of two-dimensional transition metal carbides, nitrides, and carbonitrides with highly controllable structure, composition, and surface chemistry to adjust for target applications. Here, we demonstrate the modifications of two-dimensional MXenes by low-energy ion implantation, leading to the incorporation of Mn ions in Ti3C2Tx (where Tx is a surface termination) thin films. Damage and structural defects caused by the implantation process are characterized at different depths by XPS on Ti 2p core-level spectra, by ToF-SIMS, and with electron energy loss spectroscopy analyses. Results show that the ion-induced alteration of the damage tolerant Ti3C2Tx layer is due to defect formation at both Ti and C sites, thereby promoting the functionalization of these sites with oxygen groups. This work contributes to the inspiring approach of tailoring 2D MXene structure and properties through doping and defect formation by low-energy ion implantation to expand their practical applications.