In the summer before the 2012–13 season, Tuktamysheva sustained a knee injury. She was assigned to 2012 Skate Canada International and the 2012 Trophée Éric Bompard, entering both events as the defending champion. In October, Mishin said that her participation at Skate Canada International was uncertain due to injury and growth issues. Tuktamysheva did compete in Skate Canada International, placing sixth in the short program and third in the free skate. She finished fourth overall with a total score of 168.00, just 0.04 less than bronze medalist Kanako Murakami. At the 2012 Trophée Éric Bompard, Tuktamysheva was third in the short program and second in the free skate. She obtained a personal best free skating score, 121.36 points, and won the silver medal ahead of teammate Yulia Lipnitskaya. Tuktamysheva qualified for the Grand Prix Final in Sochi, Russia, where she was fifth in the short program and second in the long, finishing fifth overall. At the 2013 Russian Championships, also held in Sochi, she placed first in the short program but fell ill with a cold before the free skate. Mishin initially indicated that she would withdraw but later she and her team decided she would compete. Tuktamysheva said, "I might find myself in an even worse situation in the future. I have to know how to handle it, so we decided to skate." She finished first in the free skate and won her first senior national title.