Due to its capacity to achieve nanometer-scale machining and lithography, focused ion beam (FIB) is an extended tool for semiconductor device fabrication and development, in particular, for diamond-based devices. However, some technological steps are still not fully optimized for its use. Indeed, ion implantation seems to affect the crystalline structure and electrical properties of diamond. For this study, a boron-doped ([B] ~ 1017 atoms·cm-3) diamond layer grown by CVD was irradiated using Ga+ by FIB, with 1nA current and 5, 20, and 30 keV of acceleration voltage. The Ga+ implanted diamond layer has been analysed through cathodoluminescence (CL) and scanning transmission electron microscopy (STEM)-related techniques. The beam penetration depth has been simulated by Monte Carlo calculations of both Ga+ (FIB) and e- (CL) beams at different energies. The comparative CL analysis of the layer as-grown and after implantation revealed peaks related to defects, such as A band, H3 center, and defects present in the green band region. The STEM studies for the 30 keV implanted sample showed that the diamond lattice is affected by the damage, evidencing amorphisation in the layer with a sp2/sp3 ratio of 1.37, estimated by EELS. Therefore, this study highlights the effects of the Ga+ implantation on the optical and structural characteristics of diamond, using different methods.