Once nanomaterials have been synthesized, inducing further structural modifications is challenging. However, being able to do so in a controlled manner is crucial. In this context, germanium nanowires are irradiated in situ within a transmission electron microscope (TEM) by a 300 keV xenon ion beam at temperatures ranging from room temperature (RT) to 500 °C. The ion irradiation is performed in situ and the evolution of nanowires during irradiation is monitored. At 300 °C and below, where the temperature is low enough to allow amorphization, the ion beam causes the formation of nanostructures within the nanowires. Formation of nanopores and swelling of nanowires is observed for a very low fluence of 2.2 × 1014 and up to 4.2 × 1015 ions cm−2. At higher fluences, the thickness of the nanowires decreases, the nanowires lose their wire-like cylindrical shape and the nanostructuring caused by the ion beam becomes more complex. The nanostructures are observed to be stable upon crystallization when the nanowires are annealed at 530 °C. Furthermore, in situ imaging allows the growth of nanopores during irradiation to be followed at RT and at 300 °C providing valuable insights into the mechanism responsible for the nanostructuring.