Their 1990 EP, Dumb Ask, was produced by Steve Albini, and following this the group signed to British label Neat Records. However, the album was pressed poorly and the group severed its ties to the label, and went back to recording for Complacency Records with Bonnet, who by that time had joined the group on guitar. Block left the band in 1992 and was replaced by Dan Forden, after which the group returned to the studio. 1994 saw the group releasing The Why Album and working on a local Chicago public access television show called Cool Clown Ground. Albini recorded the group's next release, Not a Food (which had actually been recorded in July 1994 but which did not see release until 1996). Shortly after these sessions Forden left the band; filling his shoes was Dylan Posa (formerly of The Flying Luttenbachers). By this time Cheer-Accident members were collaborating regularly with other Chicago indie artists such as U.S. Maple, Bobby Conn, Gastr del Sol, and Smog.
In January 1999, Phil Bonnet died of a brain aneurysm while the group recorded material for its eighth album, Salad Days. The group decided to continue on; Jamie Fillmore filled Bonnet's role as guitarist, and a 1997 recording session, which yielded a 52-minute song called "Trading Balloons", was released as an EP. Salad Days was finally released on Skin Graft Records in October 2000. In 2003, the group recorded another full-length for Skin Graft, Introducing Lemon, as well as a soundtrack CD to a comic book called Gumballhead the Cat.