He often collaborates with fellow director John Musker and is best known for writing and directing the Disney animated films The Great Mouse Detective (1986), The Little Mermaid (1989), Aladdin (1992), Hercules (1997), Treasure Planet (2002), The Princess and the Frog (2009), and Moana (2016).

[3] In 1982, Clements proposed adapting the children's book series Basil of Baker Street by Eve Titus into an animated feature and, along with story artist Pete Young, it was pitched to Ron Miller.

Due to a shortened production schedule and multiple story rewrites, Roy E. Disney assigned Mattinson to serve as director/producer while Clements was brought in as another director.

[5] While working on The Great Mouse Detective, newly appointed Disney CEO and chairman Michael Eisner and Jeffrey Katzenberg issued invitations to the animation staff for their first held "gong show" session.

[11] The directors chose Aladdin because they thought the story would suit a wackier, faster-paced, and more contemporary mood than that found in then-recent Disney animated films.

[12] Working from Ashman and Menken's treatment and musical score, the two delivered a story reel to Katzenberg in April 1991, which was strongly disapproved of.

[18] Following Treasure Planet, Clements and Musker later inherited Fraidy Cat, which was originally a project developed by Dutch animation director Piet Kroon.

[24] After directing The Princess and the Frog, Clements and Musker started working on an adaptation of Terry Pratchett's Mort,[25] but obtaining the film rights prevented them from continuing with the project.

In July 2013, it was revealed that the film, titled Moana, would be "a Polynesian tale involving the island folk and the idols made famous the world over".