Development of new catalysts is seen as a crucial element for securing energy resources and for better protection of the environment. However, progress in the fundamental understanding of catalysts is often lacking and, furthermore, the detailed control of materials on the nanoscale is of essence. We pursue the goal of understanding catalytic processes by focusing on what happens on the atomic-level. Scanning Probe Microscopies (SPMs) are particularly strong techniques in this regard, since they allow us to resolve surfaces and nanoparticles atomically and sometimes directly inspect the intermediate stages of a chemical reaction. We have successfully used the scanning tunneling microscope (STM) to investigate models of catalysts. The so-called hydrodesulfurization catalyst is a very important catalyst used in oil refineries worldwide for upgrading crude oil and removing sulfur impurities to prevent pollution (acid rain). The catalyst mainly consists of so-called single-layer MoS₂ nanoparticles, and we can reveal in atom-resolved STM images how S-containing molecules representative of the oil interact and react on the surface of the MoS₂ nanoparticles [1]. We also investigate novel metal-oxide nanostructures [2] from earth-abundant transition metals (Co, Ni), which are promising replacements of typical expensive noble metals for catalytic water splitting for hydrogen production. I will show how we can follow the first steps of this reaction in STM movies, by in-situ monitoring water dissociation and subsequent hydrogen diffusion.