Choate moved to the Montreal Expos, during the 2003/ off-season, but didn't get to play a game in the last-ever season for the Expos, as the Arizona Diamondbacks acquired him in a trade on March 27, that sent Arizona pitcher John Patterson back to Le Stade Olympique. Choate appeared in nearly every second game for the D-Backs, playing 74 games (the most number of games by a left-handed pitcher in Diamondbacks history and the 4th highest in total franchise history), achieving a 2-4 record with a 4.62 ERA.
In and , Choate played in 90 games. However, Choate played a vast majority of the 2006 season with Arizona's Triple-A affiliate, the Tucson Sidewinders, playing a key role in the bullpen, by helping them win the Pacific Coast League championship.
Choate later signed a minor league contract with the Minnesota Twins on January 9, , but chose to become a free agent on March 24 after being reassigned to a minor league camp three days earlier. He signed a minor league contract with the Diamondbacks in April 2007, and was assigned to Triple-A Tucson. The Diamondbacks purchased his contract from Tucson on June 26, 2007, but he made only two appearances before he was designated for assignment on June 28.
On November 14, 2007, the Milwaukee Brewers signed Choate to a one-year contract. During spring training , Choate broke a bone in his left hand. In mid-June, he began his rehab assignment in the minors. He pitched for the first time in the 2008 season for the Class A-Advanced Brevard County Manatees. He was next moved up to Triple-A Nashville. On July 10, Choate was sent outright to the minors.