The development of metal-N-C materials as efficient non-precious metal (NPM) catalysts for catalysing the oxygen reduction reaction (ORR) as alternatives to platinum is important for the practical use of proton exchange membrane fuel cells (PEMFCs). However, metal-N-C materials have high structural heterogeneity. As a result of their high-temperature synthesis they often consist of metal-N sites and graphene-encapsulated metal nanoparticles. Thus it is hard to identify the active structure of metal-N-C catalysts. Herein, we report a low-temperature NH Cl-treatment to etch out graphene-encapsulated nanoparticles from metal-N-C catalysts without destruction of co-existing atomically dispersed metal-N sites. Catalytic activity is much enhanced by this selective removal of metallic nanoparticles. Accordingly, we can confirm the spectator role of graphene-encapsulated nanoparticles and the pivotal role of metal-N sites in the metal-N-C materials for ORR in the acidic medium.