General manager Syd Thrift was impressed with Bowden and asked him to join the Pirates' baseball operations department as an administrator.
[citation needed] Bowden was named Major League Executive of the Year in 1999 by The Sporting News after leading one of the lowest payroll teams in baseball to 96 wins.
[citation needed] In 1998 Bowden traded Jeff Shaw to the Los Angeles Dodgers for infielder Paul Konerko and left-hander Dennys Reyes.
"[9] However, the Shaw-Konerko trade turned out to be a lopsided one, with Konerko making six All-Star teams in his career (later with the White Sox).
[11] Bowden is perhaps best known for his drafting of Joey Votto, Adam Dunn, and Aaron Boone, and his trades for Ken Griffey Jr. Denny Neagle, John Smiley, Kevin Mitchell, Deion Sanders, José Guillén and Alfonso Soriano.
[citation needed] After he was fired by Cincinnati, Bowden worked as a commentator on ESPN before being hired by Major League Baseball to serve as GM of the Montreal Expos, who were soon to become the Washington Nationals, in November 2004.
In 2006, Bowden traded Gary Majewski from the Nationals to the Reds along with Bill Bray, Royce Clayton, and Brendan Harris for Austin Kearns, Felipe López, and Ryan Wagner.
[citation needed] In February 2009, it was reported that Bowden along with former special assistant José Rijo were part of an FBI federal investigation into the skimming of signing bonus money from Latin American baseball players.
His broadcasting career has also included appearances for ESPN's Cold Pizza, SportsCenter, ESPNEWS, and Baseball Tonight.
He also worked for local television and radio stations in both Cincinnati, Ohio and Washington, D.C., while he was a Major League senior VP and general manager in each respective city for a combined 15 years.