In this article, ion-beam induced effects in multi-layered III-V semiconductor structures are reviewed. Besides doping, important effects occurring during ion irradiation are defect formation and diffusion, amorphisation and intermixing. It is shown that these processes are closely related to each other. In layered systems consisting of group III-phosphides and -arsenides, which can be amorphised by ion implantation, cascade mixing is the dominant mixing mechanism at low temperatures. At a critical temperature, the crystalline structure is retained after implantation and the mixing efficiency may drop down because cascade mixing is more efficient in amorphous semiconductors than in their crystalline counterparts. A further increase of temperature results in an increase of the mixing efficiency due to thermally enhanced processes. Although much less experimental data exist on ion-beam induced effects in layered group III-nitride systems, the results suggest that these systems are not amorphised during ion implantation. In this case, the experimental results can be explained assuming recoil rather than cascade mixing to occur with the former being much weaker than the latter. A few applications of ion implantation of multi-layered semiconductor systems are addressed.