The results of O'Dowd's GM career have been mixed. Upon taking over the team, he traded fading stars Dante Bichette, Vinny Castilla, and Darryl Kile, opting to build a team around pitching, speed and defense. The following season, after a surprising 82-80 run, O'Dowd signed pitchers Denny Neagle and Mike Hampton to long-term contracts. The acquisitions turned out to be disastrous for the club and were two of the worst free-agency signings in baseball history. Afterwards, O'Dowd attempted to shed salary and build a foundation of young talent around franchise cornerstone Todd Helton. Under his watch, the team developed players such as Matt Holliday, Troy Tulowitzki, Jeff Francis, and Ubaldo Jiménez.
The 2007 season was arguably the most surprising run by any Rockies team, as the team won 21 of their last 22 games to make it to a tiebreaker against the San Diego Padres. The Rockies, who were making their first playoff appearance in 12 years, swept both the Philadelphia Phillies and Arizona Diamondbacks en route to the 2007 World Series, before losing to the Boston Red Sox. O'Dowd was rewarded with a contract extension following the team's successful playoff run. As the Rockies struggled in 2012, the Rockies restructured their front office, making Bill Geivett their director of major league operations, though O'Dowd retained the title of general manager.
On December 3, 2013, O'Dowd orchestrated what is considered among fans one of the most badly lopsided trades in franchise history, losing CF Dexter Fowler and a player to be named later to to Houston Astros for pitcher Jordan Lyles and outfielder Brandon Barnes. 
^Klis, Mike. "O'Dowd no fan of dollar dominance", The Denver Post, October 22, 2000. Accessed October 24, 2007. "He is an adult now, though, much more objective about the game and no doubt considerably less emotionally attached than his childhood buddies from Montville."