Fleshgod Apocalypse was formed during 2007 and recorded their first demo the same year. The demo was re-released the following year on a split CD with fellow Italian bands Septycal Gorge, Modus Delicti, and Onirik.
Fleshgod Apocalypse then signed to Neurotic Records. In early 2008 the band toured Europe, supporting bands like Behemoth, Origin, Dying Fetus, Hate Eternal, Suffocation, Napalm Death and many more. In May 2008, the band recorded its first full-length album, Oracles. In December of that year the band decided to part ways with Neurotic Records and signed with Willowtip Records, who released Oracles in 2009. Shortly after the release of Oracles in 2009, the band had a lineup change, with a new member, Tommasso Ricardi taking over vocals and rhythm guitar, which were previously handled by Francesco Paoli, as Paoli took over the drums at this time.
In 2010, Fleshgod Apocalypse released a new EP entitled Mafia. It includes four new tracks and a cover of the track "Blinded by Fear" by At the Gates.
Until 2010, current Fleshgod Apocalypse drummer Francesco Paoli was simultaneously in his former band Hour of Penance doing vocals, as well as drumming in Fleshgod Apocalypse. Also in 2010, another new member, Francesco Ferrini, was added to the band to play keyboards. Ferrini had previously played session keyboards on Oracles and Mafia.
In May 2011, the band signed a worldwide deal with German record label Nuclear Blast Records. The band has set the release date for their forthcoming second album, entitled Agony, as August 9, 2011. The iTunes version of Agony also includes a cover of the track Heartwork by Carcass.
Fleshgod Apocalypse is part of the 2011 Summer Slaughter Tour in North America alongside co-headliners Whitechapel and The Black Dahlia Murder. The band is set to go on tour in the US with Polish band Decapitated in late 2011.