The oxygen reduction reaction (ORR) activity for Manganese oxide (MnOx) based nanostructures primarily depend upon their morphology, phase and surface Mn valency. While used in fuel cells or metal air batteries, MnOx undergoes irreversible change with degradation in ORR activity. In the present study, we developed a methodology for electrochemical regeneration of their ORR activity by potentiostatic conditioning. MnOx nanostructures with three different morphologies were grown on N doped graphene (NG) and their ORR activity was measured in alkaline medium by rotating ring disc electrode (RRDE). The catalysts were subjected to two step electrochemical treatment and the ORR activity after each step was monitered by rotating disc electrode (RDE). In the first step, the catalysts were put to 300 electrochemical cycles in the potential window 1.12 to 0.12 V (vs. RHE), and after this step, the ORR onset potential showed negative shift, with decrease in limiting current density. On subsequent potentiaostatic treatment at −0.58 V in O2 atmosphere, partial regeneration of onset potential, electron transfer number (n) and current density were observed. The characteristic redox peaks for MnOx disappeared in the first step and reappeared after the second step. After each step, the catalysts were characterised ex-situ by X-ray diffraction (XRD), Transmission electron microscope (TEM) and X-ray photoelectron spectroscopy (XPS). It showed that after the first step the decay in ORR activity was due to phase transformation to Mn3O4 with decrease in nominal Mn valency and drastic change in microstructure. Then the activity regeneration after the second step was due to the regeneration of MnOOH phase and Mn valency.