Abstract In-situ electrochemical nitrite reduction is an established method to quantify site density (SD) of platinum-group-metal-free catalysts for PEM fuel cells. However, its poisoning mechanism remains unclear, often yielding underestimated values. Crucially, we identify a unique configuration where single metal centers adsorb two NO molecules, which challenges conventional electrochemical quantification. To resolve this, we developed an in-situ acid-assisted nitrite poisoning method (AANPM) coupled with graphene-based attenuated total reflection Fourier transform infrared spectroscopy (graphene-based in-situ ATR-FTIR). This approach quantifies SD and elucidates active site structures in transition metal-nitrogen-carbon (MNC) electrocatalysts. By incorporating the average electron transfer number for NO electroreduction (NOR), we achieve accurate SD calculations. Validated across iron/cobalt phthalocyanine molecular catalysts and pyrolyzed FeNC/CoNC materials, this method can be used to stablish structure-activity relations.