Chapman moved to Pixar in 2003 after being invited by her old colleague Joe Ranft, where she had a brief stint on Cars before beginning development on and directing Brave. Chapman conceived the project and was announced as the director of the film, making her Pixar’s first female director. In October 2010, however, she was replaced by Mark Andrews following creative disagreements between her and John Lasseter. There were rumors that she subsequently left Pixar, but she remained on staff until shortly after the release of Brave, and started work as a consultant at Lucasfilm at the end of July 2012, where she helped solve story problems of Strange Magic. When asked whether she will return to Pixar, Chapman responded by saying she has no desire to go back there feeling that: “The atmosphere and the leadership doesn’t fit well with me.”

In 2013, she returned to her old employer, DreamWorks Animation, where she helped in developing Rumblewick that had a strong female protagonist and was described as “funny with magic and heart.” Chapman then left DreamWorks shortly afterwards though. As of 2016, she is developing projects for Chapman Lima Productions, with her husband Kevin Lima.

Chapman is married to director Kevin Lima (A Goofy Movie, Tarzan, Enchanted), whom she met at California Institute of the Arts. They have a daughter, Emma Rose Lima, who was the inspiration for Mérida, Brave’s young princess. They reside in Tamalpais Valley, California. Chapman claims Scottish ancestry. In 2014, Chapman urged Scots to back independence in the September referendum.

In May 2016, it was reported that Chapman would make her live-action directorial debut with Come Away, a fantasy drama that serves as a prequel to Alice in Wonderland and Peter Pan. In May 2018, it was reported that Angelina Jolie and David Oyelowo were cast to play the parents of Alice and Peter, with Jolie and Oyelowo also serving as producers. Anna Chancellor and Clarke Peters joined in August, with filming in London starting that same month.

In February 2020, it was reported that Chapman was attached to write and direct a live-action hybrid film adaptation of Ghost Squad.