During their hiatus, Bower played with Down and drummed for Crowbar, while Patton played with death metallers Silent Green, and Williams picked up a pen to write for Metal Maniacs magazine.
When the band regrouped with Vince LeBlanc on bass they recorded what would become considered as their best work, Dopesick (1996). Produced with the help of Billy Anderson (who had worked with the mentors Melvins) Eyehategod managed to delve into even deeper depths of hardcore depression (sonically speaking), while rising their music higher above their noise of the past. After, however and once again, the band took a break with Bower returning to Crowbar. The period was not completely void, however, as several singles were released during the time. The period was summed up on the Southern Discomfort compilation in 2000.
Now with Daniel Nick replacing LeBlanc, Eyehategod would return in 2000 again to torture their instruments on Confederacy of Ruined Lives even though their style was starting to sound tired. It would be followed up in 2001 with 10 Years of Abuse (and Still Broke), gathering together a 1990 demo, a 1994 radio broadcast, and a 2000 European live performance.
2000's Confederacy of Ruined Lives was a much more polished, sober affair, sounding more like a sequel to Take as Needed for Pain.
Following the aftermath of Hurricane Katrina, Williams and his ex-girlfriend Alicia Morgan (a member of metal band, 13) were arrested in Morgan City, Louisiana on a narcotics charge. Williams spent 91 days in the Morgan City Jail, but kicked his heroin habit. With the help of his band mates and supporters such as Phil Anselmo (ex-(Pantera, Down, Superjoint Ritual)), Williams was released from jail on December 2, 2005.
In 2007, 'Emetic Record's released a various artists tribute album to Eyehategod, titled For the Sick.
LaCaze died on August 23, 2013 from respiratory failure. He would be replaced by Aaron Hill.
2014 saw their self-titled full-length album Phil Anselmo's 'Housecore Records' label released; it was the last featuring Joey LaCaze.
During 2016 Williams would be replaced by Phil Anselmo for live events due to heath matters that would end off seeing him receive a liver transplant later that year. The next release, A History of Nomadic Behavior followed in 2021.