After these projects, Dindal left Disney briefly to work on outside projects. He returned to the studio in 1987 and got his first head role as an animator for Disney's The Little Mermaid. He later worked as head animator for the movie The Rescuers Down Under. He directed the animated effects for the live-action 1991 film The Rocketeer, and got a job in the 1992 animated film Aladdin.
Dindal's directorial debut was Cats Don't Dance, which was released in 1997, three years before The Emperor's New Groove was released in 2000. In Cats Don't Dance Dindal voiced a minor character. Although the film wasn't publicly successful, it won the Annie Award for Best Animated Film and Dindal was nominated for directing. The Emperor's New Groove was initially expected to be a classic Disney musical feature called Kingdom of the Sun. However, that idea didn't work out, and Dindal, along with Chris Williams and David Reynolds, drastically changed the script to a comedy. During the six-year production, he started to work on Cats Don't Dance, a Turner Broadcasting (since merged into Warner Bros.) animated musical production.
Dindal worked on Chicken Little, another Disney production, which needed a huge animation team. The movie was a moderate financial success, yet received negative reviews, and is currently the worst rated film of the Disney animated canon at Rotten Tomatoes with a score of 36%. Dindal had two small voice roles in the film. The movie was nominated to several Annies, but Dindal was not nominated as a director. During the movie's production, Disney produced Kronk's New Groove as a direct-to-video feature. Dindal was working on Chicken Little, so he didn't get a position on the staff. Later, Dindal created The Emperor's New School.
In March 2006, a day after the DVD release of Chicken Little, Dindal left Disney, reportedly because he was "tired of dealing with then-WDFA head, David Stainton." In the next few years, he was attached as a director to several live-action films, including Sherlock's Secretary,Kringle, and Housebroken. In December 2010, DreamWorks Animation announced that Dindal was directing Me and My Shadow, a 3D feature film combining both computer and traditional animation. In January 2012, it was reported that he was no longer directing the film, and that he was replaced by Alessandro Carloni. As of May 2015, Dindal and screenwriter David Reynolds are attending a conversation event for the Austin Film Festival on June 7th, 2015.