In the pursuit of more efficient heterogeneous catalysts and electrocatalysts, the real-space observation of active sites at the atomic scale under reaction conditions opens exciting possibilities for establishing detailed composition–structure–reactivity relationships. In this work, we focus on the study of small oxide clusters of the early transition metals tungsten and molybdenum using electrochemical scanning tunnelling microscopy (EC-STM). The metal oxide clusters are generated directly in the aqueous electrolyte, with the metals acting as ‘electrochemical evaporator’, and this process is studied through a combination of cyclic voltammetry, electrochemical impedance spectroscopy, inductively coupled plasma–optical emission spectroscopy and high-resolution mass spectrometry. Once the transition metal oxide clusters are generated, we immobilise them on boron nitride nanomesh, a corrugated monolayer of hexagonal boron nitride on Rh(111) with unique molecular trapping properties. The immobilisation of the oxide clusters is experimentally verified using ex situ X-ray photoelectron and Raman spectroscopy, also gauging any chemical changes of the clusters compared to the dispersed state in aqueous environment. Finally, we use EC-STM to directly observe the tungsten and molybdenum oxide cluster-decorated nanomesh surface in the presence of electrolyte under electrochemical potential control. To the best of our knowledge, this is the first study where molybdenum tips have been used for EC-STM observation. By imaging tungsten oxide clusters with Mo tips and vice versa, we explore the stable combinations of substrate and tip materials and potentials towards chemically selective imaging at the atomic scale. Moving forward, we will use this knowledge to develop operando electrochemical imaging while an electrocatalytic reaction is ongoing.