Malone made the jump to professional acting with the 1996 film Bastard Out of Carolina. She was nominated for the Independent Spirit Award for Best Debut Performance and a Screen Actors Guild Award for Outstanding Performance in a TV Movie or Miniseries for this role. From there, her roles have grown to include several Hollywood features. In 1997, she was nominated for a Golden Globe, Best Actress in a Mini-Series or TV Movie, for her role in Hope. After several years of home schooling, she briefly attended the Professional Children's School in New York, but did not last long. In January 2000, Malone won legal emancipation from her mother, to bar maternal interference with her career and earnings; Malone has said that her mother "mismanaged" some of her earnings.

Malone co-produced the 2002 film American Girl, a drama in which she also acted. She was due to feature in the film Vinyl, but had to withdraw due to filming conflicts, and was replaced by Michelle Trachtenberg. She h