Allegaeon was formed in the early summer of 2008. They initially played small shows, at bars and houses in and around Fort Collins. In August 2008 they independently released a self-titled EP. Soon after, they signed with Metal Blade Records. In January 2010, Allegaeon entered the studio to record their debut album Fragments of Form and Function. The album was released in July 20 of 2010 through Metal Blade. In January 2012, Allegaeon went to Lambesis Studios in December 2011, in San Diego, California to record their second full-length album Formshifter. Formshifter was released May 8 of 2012 through Metal Blade. In 2013, founding guitarist Ryan Glisan collaborated on a project with Tim Lambesis, and left the band shortly thereafter. He was replaced by Michael Stancel.

Their third full-length album, titled Elements of the Infinite, was released June 24 of 2014 through Metal Blade. The album has been heavily praised, with Gregory Heaney of allmusic calling it a "creative breakthrough" and praising "the dazzling guitar work" and "epic orchestral flourishes".In 2015, original vocalist Ezra Haynes departed Allegaeon, not citing a specific reason, though it is clear it wasn't because of internal band issues.  Riley McShane was immediately selected to take over as vocalist, and has received a positive reaction from the fans. In June 2016, Allegaeon will release their fourth studio album, according to a response on Twitter //more