At the 2013 Russian national championships, Mustafina successfully defended her all-around title with a score of 59.850, earning a 15.450 on beam, 15.500 on bars, 13.600 on floor, and 15.300 on vault. These scores qualified her to the balance beam and uneven bars finals in first place, and to the floor exercise final in third place, but she withdrew from all but the bars final to protect her knee. She received a silver medal with the Moscow Central team and finished third in the uneven bars final, behind Anastasia Grishina (first) and Tatiana Nabieva (second).
At the 2013 European Championships in Moscow, she fell twice off the balance beam in qualifications and entered the all-around final in fourth place, with a score of 56.057. In the final, she scored 15.033 on vault, 15.133 on uneven bars, 14.400 on balance beam, and 14.466 on floor, winning the all-around title—her first individual European title—with a total of 59.032. The next day, she won the uneven bars final with a score of 15.300. She also qualified to the floor exercise final in third place, but withdrew and gave her spot to Grishina, who had been left out of the final due to the limit of two gymnasts per country.