Single-atom catalysts (SACs) have become a prominent theme in heterogeneous catalysis, not least because of the potential fundamental insight into active sites. The desired level of understanding, however, is prohibited due to the inhomogeneity of most supported SACs and the lack of suitable tools for structure-activity correlation studies with atomic resolution. Herein, we describe the potency of electrospray ionisation mass spectrometry (ESI-MS) to study molecularly defined SACs supported on polyoxometalates in catalytic reactions. We were able to identify the exact composition of active sites and their evolution in the catalytic cycle during CO and alcohol oxidation reactions performed in the liquid phase. Critical information on metal-dependent reaction mechanisms, the key intermediates, the dynamics of active sites and even the stepwise activation barriers were obtained, which would be challenging to gather via prevailingly adopted techniques in SAC research. DFT calculations revealed intricate details of the reaction mechanisms, and strong synergies between ESI-MS defined SAC sites and electronic structure theory calculations become apparent.