Pruett broke into the industry in 1989 as Bob Burden's assistant on Flaming Carrot Comics, where he inked backgrounds, assisted on lettering, and transcribed scripts. He worked with Burden from issues #23-29.
In 1992 Joe joined Gary Reed's Caliber Comics where he served through 1998 as a writer, an editor, and a creative director. While at Caliber, Joe's anthology title, Negative Burn, was nominated for numerous Harvey and Eisner awards.
In 1998 He left Caliber to become a freelance writer and became a regular contributor to Marvel's X-Men books. In particular he wrote Cable during the storylines "The Twelve" and "Ages of Apocalypse".
Pruett formed Desperado Publishing in the summer of 2004 and brought back the second series of Negative Burn. He is launching a third series of yearly anthology books in 2010.