In this article we detail the application of electron microscopy to visualise discrete structural transitions incurring in single crystalline Ge nanowires upon Ga-ion irradiation and subsequent thermal annealing. Sequences of images for nanowires of varying diameters subjected to an incremental increase of the Ga-ion dose were obtained. Intricate transformations dictated by a nanowire's geometry indicate unusual distribution of the cascade recoils in the nanowire volume, in comparison to planar substrates. Following irradiation, the same nanowires were annealed in the TEM and corresponding crystal recovery followed in situ. Visualising the recrystallisation process, we establish that full recovery of defect-free nanowires is difficult to obtain due to defect nucleation and growth. Our findings will have large implications in designing ion beam doping of Ge nanowires for electronic devices but also for other devices that use single crystalline nanostructured Ge materials such as thin membranes, nanoparticles and nanorods.