On-chip electrocatalytic microdevices (OCEMs) are an emerging electrochemical platform specialized for investigating nanocatalysts at the microscopic level. The OCEM platform allows high-precision electrochemical measurements at the individual nanomaterial level and, more importantly, offers unique perspectives inaccessible with conventional electrochemical methods. This protocol describes the critical concepts, experimental standardization, operational principles and data analysis of OCEMs. Specifically, standard protocols for the measurement of the electrocatalytic hydrogen evolution reaction of individual 2D nanosheets are introduced with data validation, interpretation and benchmarking. A series of factors (e.g., the exposed area of material, the choice of passivation layer and current leakage) that could have effects on the accuracy and reliability of measurement are discussed. In addition, as an example of the high adaptability of OCEMs, the protocol for in situ electrical transport measurement is detailed. We believe that this protocol will promote the general adoption of the OCEM platform and inspire further development in the near future. This protocol requires essential knowledge in chemical synthesis, device fabrication and electrochemistry.