Being able to access the rich atomic-scale phenomenology, which occurs during the reactions pathways, is a pressing need toward the pursued knowledge-based design of more efficient nanocatalysts, precisely tailored atom by atom for each reaction. However, to reach this goal of achieving maximum optimization, it is mandatory, first, to address how exposure to the experimental conditions, which will be needed to activate the processes, affects the internal configuration of the nanoparticles at the atomic level. In particular, the most critical experimental parameter is probably the temperature, which among other unwanted effects can induce nanocatalyst aggregation. This work highlights the high potential of experimental techniques such as the scanning probe microscopies, which are able to investigate matter in real space with atomic resolution, to reach the key challenge in heterogeneous catalysis of achieving access to the atomic-scale processes taking place in the nanocatalysts. Specifically, the phenomenology occurring in a nanoparticle system during annealing is studied with atomic precision by scanning tunneling microscopy. As a result, the existence of an internal atomic restructuring, occurring already at relatively low temperatures, within Ir nanoparticles grown over h-BN/Ru(0001) surfaces is demonstrated. Such restructuration, which reduces the undercoordination of the outer Ir atoms, is expected to have a significant effect on the reactivity of the nanoparticles. Going a step further, an internal restructuring of the nanoparticles during their involvement as catalysts has also been also identified.