A new approach in electrode catalysis bearing immense potential for electrochemical technologies is the prospect of carbon based electrodes. Pristine carbon nanostructures are relatively inert and modications including nitrogen, boron, sulfur doping and their combinations are known for their beneficial effects on the electrochemical activity of carbon nanomaterials in both alkaline and acidic media. However, long-term stability of these materials, especially in acidic environment, is rarely mentioned. Here, we evaluate the stability and longterm degradation of nitrogen (N), sulfur-nitrogen (SN), and boron-nitrogen (BN) co-doped graphene akes as oxygen reduction electrocatalyst with theoretical and experimental techniques. We assume that nitrogen dopants in the graphene sheet interact with electrons and protons at the electrode-electrolyte interface leading to ammonia scission and continuous catalyst deactivation. We analyse and compare the ammonia scission pathways of N, BN and SN containing graphene structures by the use of Density Functional Theory (DFT) B3LYP method. The stability of the model systems with regard to the investigated reaction pathway are correlated with the HOMO-LUMO energy separation, spin and charge densities showing that degradation of doped graphene and oxygen reduction reaction is driven by similar material parameters. The computational results are corroborated with electrochemical measurements at SAFC operating conditions.