In 1998, Project 86 released its self-titled debut on BEC Recordings, a sublabel of Tooth & Nail Records. Immediately the band was labeled "rapcore". Though Schwab's vocals could barely be called rapping, it was a convenient label due to the popularity of that genre of music at the time. After putting out their second album Drawing Black Lines (2000), the band was taken on by Atlantic Records. However, the promised re-release of Drawing Black Lines went from being a full-fledged reissue with new artwork and three new songs to nothing more than a bare bones repackaging of the exact same album.

At the outset of its career, Project 86 shared the stage with P.O.D. and Blindside on the Warriors Tour. Project (as the band is often referred to by its fans) has played mainstage at both Christian and secular festivals, and has shared the stage with other well known bands such as Queensrÿche, Linkin Park, Dead Poetic, and Stavesacre.

The next two years saw Project 86's addition of a second guitarist (Cory Edelman, formerly of No Innocent Victim) and his subsequent departure just a few months later. Also, influential rocker Marilyn Manson took interest in the band and had the song "P.S.", originally released on Drawing Black Lines, added to the Blair Witch 2 soundtrack. Probably due to this interest, Project 86 became a higher priority for Atlantic. Atlantic poured over half a million into Project's next musical foray, entitled Truthless Heroes (2002), which, though proving to be the band's most popular outing yet, was released amidst some turmoil.

Over the course of recording Truthless Heroes (which took around a year to complete) Project 86 had increasing difficulty with its management, as well as both record labels (Tooth & Nail still had rights to release their music to the Christian market). This wore the band down immensely, but by the time the album was finished, the difficulty seemed to have worked out in Project's favor - Atlantic bought all of Tooth & Nail's remaining rights to the band and released "Hollow Again", the first single from the album, on mainstream radio. Word came out that the band would be shooting a video for the song shortly, but it never materialized as Atlantic ran into troubles of its own and liquidated some of its assets - including Project 86. In 2003, finding themselves cut loose by both label and management, Project started its own independent label.

Project 86's fourth album, Songs To Burn Your Bridges By, was released independently in the fall of 2003 and went on to sell relatively well despite being sold only at shows and online. Come 2004, they re-signed to Tooth & Nail and Songs To Burn Your Bridges By was re-issued with three new songs and completely new artwork.

In February 2005, Project 86 announced that they were working on a new album. The title was later announced as ...And The Rest Will Follow. The band spent several weeks in the studio with Garth Richardson over the summer recording the material, and then began releasing a new song every Monday on their purevolume site. The album was released on September 27, 2005, and sold 8,000 copies in its first week, more than any other Project 86 album. A release tour began September 23, with Spoken, Number One Gun, Mourning September, and The Fold.

On December 17, 2006, The band released remixes of "Something We Can't Be" and "From December" on their Myspace page. "From December" features Joseph Milligan from Anberlin on guitar and Timothy McTague from UnderOath on drums. "Something We Can't Be" was remixed by The Echoing Green.

The band's sixth full-length album, Rival Factions, was released on June 19th, 2006 through Tooth & Nail Records. The album was released in stores with artwork that varied when viewed through different colored jewel cases, and on iTunes with a bonus song not available on the standard release.