In 2005, after rejecting an offer to become the bench coach of the Florida Marlins with a guarantee to become the team's manager in 2006 (although he would eventually get that job anyway), he became the Yankees' bench coach. He even managed a game during a Joe Torre suspension, which the Yankees lost against the last place Kansas City Royals. Girardi remained the host of Kids on Deck in 2005, having shot his shows before Spring Training. YES promoted Kids on Deck during games by showing Girardi on camera sitting in the dugout during breaks in the game.

Managerial career

After the 2005 regular season, Girardi was named the manager of the Florida Marlins, replacing departed manager Jack McKeon. His first notable action as manager was to prohibit facial hair, which is a policy similar to that of George Steinbrenner, owner of the New York Yankees.

As a first-time manager for the Marlins, Girardi guided the team into surprising wild card contention (finishing with a 78-84 record) even though the team had the lowest payroll in Major League Baseball, at approximately $14 million for 2006. Despite the success Girardi achieved in his first year as manager, he was nearly fired in early August when he got into a vocal (and visible) argument with Marlins owner Jeffrey Loria.

On October 3, 2006, the Marlins announced that they had fired Girardi, presumably because of his rift with Loria. At first, Girardi was thought to be among the leading candidates to replace Yankee manager Joe Torre after a bitter postseason loss, but Torre remained with the Yankees. He was also a candidate for the Chicago Cubs manager position, interviewing for the position just days after leaving the Marlins. With his playing experience in Chicago, he was considered a front-runner for the position even before the season was over. However, the Cubs chose to go with veteran manager Lou Piniella. Girardi took himself out of the running for the Washington Nationals managerial job shortly thereafter and will return to the broadcast booth for the YES network in 2007. Despite Girardi's firing, he was rewarded for his relative success with the Marlins in 2006 with the National League Manager of the Year Award.