In situ transmission electron microscopy (TEM) of samples in a controlled gas environment allows for the real time study of the dynamical changes in nanomaterials at high temperatures and pressures up to the ambient pressure (105 Pa) with a spatial resolution close to the atomic scale. In the field of catalysis, the implementation and quantitative use of in situ procedures are fundamental for a better understanding of the behaviour of catalysts in their environments and operating conditions. By using a microelectromechanical systems (MEMS)-based atmospheric gas cell, we have studied the thermal stability and the reactivity of crystalline cobalt nanostructures with initial ‘urchin-like’ morphologies sustained by native surface ligands that result from their synthesis reaction. We have evidenced various behaviors of the Co nanostructures that depend on the environment used during the observations. At high temperature under vacuum or in an inert atmosphere, the migration of Co atoms towards the core of the particles is activated and leads to the formation of carbon nanostructures using as a template the initial multipods morphology. In the case of reactive environments, for example, pure oxygen, our investigation allowed to directly monitor the voids formation through the Kirkendall effect. Once the nanostructures were oxidised, it was possible to reduce them back to the metallic phase using a dihydrogen flux. Under a pure hydrogen atmosphere, the sintering of the whole structure occurred, which illustrates the high reactivity of such structures as well as the fundamental role of the present ligands as morphology stabilisers. The last type of environmental study under pure CO and syngas (i.e. a mixture of H2:CO = 2:1) revealed the metal particles carburisation at high temperature.