Born in Rye, New York, but raised in Scottsdale, Arizona, Allers became a fan of animation, at the age of five, after seeing Disney's Peter Pan. Deciding that he wanted to pursue a career at Disney and even work alongside Walt Disney himself, a few years later, he was sent off to Disneyland for a do-it-yourself animation kit. However, Allers, by then a high school student, grew discouraged about achieving his dream when he heard of Walt Disney's death in 1966.

In 1978, he relocated to Los Angeles with Steven Lisberger to work on a feature film titled Animalympics to which he provided story work, character design and animation for the film. Three years later, Allers found work serving as part of the storyboard team for Tron, which was the first theatrical feature film he worked on. In 1980, Allers and his family moved to Toronto, Canada, where he worked for Nelvana Studios as an Animator on a feature titled Rock & Rule. Following a brief return to Los Angeles, Allers provided character design, preliminary animation, and story development for the Japanese-produced animated feature, Little Nemo: Adventures in Slumberland. For the next two years, he resided in Tokyo to serve as an animation Director overseeing the Japanese artists.

Returning to Los Angeles in 1985, he heard that Disney was looking for a storyboard Artist to work on Oliver & Company. When he applied for the job, Allers was asked to draw some sample character model sheets as a tryout, and worked on a portfolio and was hired shortly thereafter. Since then, he served as a storyboard Artist on The Little Mermaid, The Prince and the Pauper, and The Rescuers Down Under before he was appointed as Head of Story on Beauty and the Beast. When story work on Beauty was finished, Allers assisted as a storyboard Artist during the re-writing of Aladdin.

In October 1991, Allers signed on to co-direct King of the Jungle alongside its initial Director George Scribner. Allers brought on board Brenda Chapman, who would become the head of story. Afterwards, several of the lead crew members, including Allers, Scribner, Don Hahn, Chapman, and production designer Chris Sanders, took a safari trip to Hell's Gate National Park in Kenya, in order to study and gain an appreciation of the environment for the film. After six months of story development work, Scribner decided to leave the project, as he feuded with Allers and the producers on their decision to turn the film into a musical, as Scribner's intention was to make a documentary-like film more focused on natural aspects. Following Scribner's departure and dissatisfied with the original story, Allers along with Hahn, Sanders, Chapman, and Beauty and the Beast Directors Kirk Wise and Gary Trousdale conceived a new story outline for the film over the course of two days in February 1992. In April 1992, Allers was joined with Rob Minkoff who was assigned as co-director, and the title was changed to The Lion King.

Following the release of The Lion King, Allers and Writer Matthew Jacobs conceived the idea of Kingdom of the Sun, and development on the project went underway in 1994. Meanwhile, Disney Theatrical Group had begun production on the Broadway musical production of The Lion King as they had done with Beauty and the Beast. At first skeptical, Allers joined the Broadway production team, and together with Lion King co-screenwriter Irene Mecchi, they wrote the libretto for which they were both nominated the Tony Award for Best Book of a Musical. After nearly four years on Kingdom of the Sun, Allers asked to leave the project due to creative differences with co-director Mark Dindal, poorly received test screenings, and the failure to meet its promotional deadlines. Ultimately, the project was reworked into The Emperor's New Groove, and Allers left to work on Lilo & Stitch as an additional story supervisor. In 2001, he was approached by Hahn to direct the short film, The Little Matchgirl. The project underwent four years of work, and was accompanied as a bonus feature on The Little Mermaid Platinum Edition DVD.

Meanwhile, Allers pitched the Celtic folk ballad tale Tam Lin to Michael Eisner, who at the time was in a corporate struggle with Roy E. Disney. Once he recognized the project as Disney's "baby", he declined to green-light the project. In May 2003, it was announced that Allers and Brenda Chapman would direct Tam Lin for Sony Pictures Animation. However, one year later, Allers was recruited to serve as an additional Director on Open Season alongside Director Jill Culton and co-director Anthony Stacchi, featuring the voice talents of Martin Lawrence and Ashton Kutcher.

In January 2012, it was announced that Allers will oversee the narrative structure, as well as supervise the production of an animated adaptation of The Prophet. In May 2014, a work-in-progress version of The Prophet was screened at the Cannes Film Festival, and was given a limited release in August 2015.