On January 6, 2006, he was traded by the Blue Jays to the Milwaukee Brewers for pitcher Brian Wolfe. The deal was widely viewed as a salary dump for the Blue Jays after the team traded for Troy Glaus. With several players on the roster capable of playing third base (Koskie, Glaus, Eric Hinske, Shea Hillenbrand, and Aaron Hill) and no assurances of regular playing time from Blue Jays general manager J.P. Ricciardi, Koskie was traded just a year after being the Blue Jays' 2004 offseason marquee free agent signing.
While the Brewers acquired a veteran infielder with a solid glove and bat to anchor their very young infield, Koskie's later seasons were marred by injuries, including missing most of the 2006 season with post-concussion syndrome from an injury he received on July 5, 2006.