This article reviews the size-dependent structural properties of ion beam synthesized Co nanoparticles (NPs) and the influence of ion irradiation on the size, shape, phase and structure. The evolution of the aforementioned properties were determined using complementary laboratory-and advanced synchrotron-based techniques, including cross-sectional transmission electron microscopy, small-angle X-ray scattering and X-ray absorption spectroscopy. Combining such techniques reveals a rich array of transformations particular to Co NPs. This methodology highlights the effectiveness of ion implantation and ion irradiation procedures as a means of fine tuning NP properties to best suit specific technological applications. Furthermore, our results facilitate a better understanding and aid in identifying the underlying physics particular to this potentially technologically important class of nanomaterials.