Sotnikova started her season with a silver medal at the 2012 Nebelhorn Trophy. Her first GP event of the season was the 2012 Skate America. In the free skate, Sotnikova's 3Lo-2T-2Lo jump combination received no points because it was deemed an invalid element. She won the bronze medal overall behind Americans Christina Gao and Ashley Wagner. At her next event, the 2012 Rostelecom Cup, Sotnikova finished 5th. At the 2013 Russian Championships, she won the bronze medal behind Elena Radionova and Elizaveta Tuktamysheva. At the 2013 European Championships, she placed first in the short program, third in the long program, and won the silver medal overall, 0.72 points behind gold medalist Carolina Kostner. Sotnikova and bronze medalist Elizaveta Tuktamysheva were Russia's first medalists in the Europeans ladies' event since Irina Slutskaya won the title in 2006.