He then worked as a commentator on ESPN before being hired by the Nationals.
In addition to the 9/11 comments that led to his firing in Cincinnati, Bowden has been involved in several other controversies.
In 1993, he fired Reds manager and former star player Tony Perez after just 44 games. Coming on the heels of racially charged comments by Reds owner Marge Schott, the firing prompted criticism of Bowden and the team for treating Perez, one of the league's few minority managers, unfairly.
In 1998, he traded All-Star reliever and Cincinnati native Jeff Shaw to the Los Angeles Dodgers. Shaw claimed at the time that Bowden had agreed not to trade him as part of a contract that involved Shaw taking less money from the Reds than he could have gotten elsewhere. “We had a handshake deal that he wasn't going to trade me,” Shaw said. “Three months later, he traded me. ... If I had been in the room with him, I would have killed him.”
In 2000, Reds coach Ron Oester reportedly was offered the job of manager by Bowden, but that when Oester didn't accept immediately, Bowden offered the job to Bob Boone without contacting Oester. At the time, Oester called Bowden “one of the worst people in the world.”
On April 17, 2006, Bowden was arrested for drunk driving in Miami, Florida.
As the GM of the Nationals, he made a deal with the Reds in mid-season 2006 involving Gary Majewski, who received a cortisone shot shortly before the trade. In May 2007 the Reds filed a grievance claiming they didn't know they were getting damaged goods. Later it was reported by Hall of Fame Sportswriter Hal McCoy that Bowden also included in the same trade a pitcher, Daryl Thompson, who Bowden believed was injured. McCoy reported that Bowden included Thompson to "stick it" to the Reds.
Bowden's poor reputation has spread to other general managers. San Diego Padres General Manager Kevin Towers in 2005 said of Bowden, "The guy's an idiot. I won't take his calls, and I don't think many others do."
An avid Segway enthusiast, he purchased a custom version in Washington Nationals team colors for Spring Training 2008. He is currently being investigated by the FBI as part of a larger probe into the alleged skimming of player bonuses by scouts in the Dominican Republic.