In the 2012–13 season, Menshov won another silver medal at the Nebelhorn Trophy. He placed 4th at both of his Grand Prix events, the 2012 Skate America and 2012 Rostelecom Cup, setting a new personal best overall score at his second event. He won again at the 2012 NRW Trophy with an overall score of 238.63 points, more than 26 points ahead of silver medalist Michal Březina. He won the bronze medal at the 2013 Russian Championships but was not named in the Russian team for the 2013 European Championships. The decision did not contravene regulations which stated that only the top two qualified automatically and the third skater could be determined by the coaches' council. However, an appeal was signed by the president of the Saint Petersburg figure skating federation, Oleg Nilov, and some competitors. Russian Minister of Sport Vitaly Mutko ordered the executive committee of the Russian figure skating federation to review the issue. They voted to uphold their original decision. Menshov was assigned to the 2013 World Team Trophy and placed third in the short program with a personal season's best score (80.60). In the free skate, he dislocated his right shoulder attempting a triple Axel and withdrew from the event. He had sustained that type of injury only once before, four years prior.