However, due to an ankle injury sustained in training before the competition began, she was only able to compete on one event, the uneven bars. In spite of her injury, in the qualification round, Liukin's bars set earned a 16.2, the highest score of any competitor on any apparatus in the meet.
Liukin's ankle injury required surgery, and the recovery period kept her out of both national and international competition for much of the year. In July 2007, although she was still recovering from her injury, she returned to competition as a member of the American team for the Pan Am Games in Rio de Janeiro. She competed only on bars and beam, contributing to the team's gold medal finish and winning an individual silver medal in the uneven bars finals and an individual silver medal on the balance beam final.

Despite limited training time on floor and vault in the summer of 2007, Liukin opted to compete all-around at the 2007 U.S. National Championships. She posted the highest score of the entire meet on bars and the second highest score on beam on the second day of competition, winning the senior bars title for the third year in a row and placing second on beam. However, she also suffered several falls and errors on floor and vault, and finished in third place overall, more than five points behind Shawn Johnson, the all-around gold medalist.
Liukin's first meet of the 2008 season was the American Cup in New York City, where she defeated 2007 winner Shawn Johnson to regain her title. She posted the highest score of the meet, a 16.600 on the uneven bars.
In March 2009 Liukin was announced as one of 12 semifinalists for the AAU Sullivan Award. The annual award honors the athlete who best represents "the qualities of leadership, character, sportsmanship, and the ideals of amateurism". On April 15, 2009, Liukin's Olympic teammate Shawn Johnson won the AAU Sullivan Award.
Liukin decided that she was not done with gymnastics and made her first post-Olympics competitive appearance at the CoverGirl Classic, where she competed only on balance beam. She placed 2nd behind teammate Ivana Hong. Liukin thought about competing uneven bars and beam at the U.S. Championships, but decided to once again just perform on beam. She placed 4th and looked on track to possibly make a fourth World Championships team. Liukin was added to the National Team and included in the World Championships selection camp. However, she pulled out of Worlds selection consideration because she felt that she was not quite up to World Championships standards.
It was announced prior to the 2011 World Gymnastics Championships that Nastia was planning a comeback to competitive gymnastics. She stated that instead of going for the all around, she would concentrate on balance beam and uneven bars, an area where the U.S. had been weak. She targeted the 2012 Covergirl Classic for her debut. Nastia was also part of the selection committee for the 2011 world team.

Outside of competitive gymnastics, Liukin had cameo roles in the April 2006 Touchstone Pictures film Stick It, a 2008 episode of Gossip Girl and a quick cameo appearance on the newest Bravo TV show, NYC Prep. She has expressed a desire to become an actress in the future. Following the Beijing Olympics, Liukin appeared on many talk shows in the United States, including The Tonight Show with Jay Leno, Late Night With Conan O'Brien, and the Oprah Winfrey Show.

She also appeared in the second season of Make It or Break It.