The structural stability of transition metal nanoclusters has been scrutinized with in situ transmission electron microscopy as a function of temperature. In particular iron, cobalt, niobium, and molybdenum clusters with diameters around 5 nm have been investigated. During exposure to air, a thin oxide shell with a thickness of 2 nm is formed around the iron and cobalt clusters, which is thermally unstable under moderate high vacuum annealing above 200 °C. Interestingly, niobium clusters oxidize only internally at higher temperatures without the formation of an oxide shell. They are unaffected under electron beam irradiation, whereas iron and cobalt undergo severe structural changes. Further, no cluster coalescence of niobium takes place, even during annealing up to 800 °C, whereas iron and cobalt clusters coalesce after decomposition of the oxide, as long as the clusters are in close contact. In contrast to niobium, molybdenum clusters do not oxidize upon annealing; they are stable under electron beam irradiation and coalesce at temperatures higher than 800 °C. In all cases, the coalescence process indicates a strong influence of the local environment of the cluster.