Lima finally got his opportunity to direct at Disney, where he directed two animated films, A Goofy Movie, and Tarzan. Wanting to direct live-action films, Lima once again left Disney, but soon returned. Thanks to Glenn Close, who voiced Kala in Tarzan, Lima was offered to direct her on 102 Dalmatians, which had just lost its Director. After directing his first live action film, he went on to direct two TV films starring Julie Andrews, Eloise at the Plaza and Eloise at Christmastime. Since 2000, Lima had wanted to make the film Enchanted, but he was repeatedly turned down because of the script being too dark, and that he was not "funny enough to do this film". The toned down script finally got green-lit, and in 2007 Enchanted was released to a positive critical reception.

Since directing Enchanted, Lima has been set to direct several projects including a live-action feature adaptation of the classic tale of Tom Thumb entitled Thumb, a film based on the popular Candy Land board game, a remake of the 1964 film The Incredible Mr. Limpet, a comedy film starring Hugh Jackman titled Avon Man, and an untitled live-action/CG film for Sony Pictures Animation. In July 2011, DreamWorks Animation announced that Lima will direct Bollywood Superstar Monkey, a Bollywood-style animated musical adventure inspired by the Indian epic tale Ramayana, and told through the point of view of its monkeys. A. R. Rahman is composing the music and Stephen Schwartz is writing the lyrics for the film. In September 2012, it was announced that the film would be released on December 19, 2015, but was half a year later rescheduled to March 18, 2016. In June 2014, the release date was pushed back to March 10, 2017. In January 2015, it was confirmed that the film was placed back into development with no release date attached.