As the 2009 season wore on, regular catcher Carlos Ruiz spent some time recuperating from an injury, allowing Bako expanded playing time near the end of the season. From September 18 to 29, Bako played in all but one of the team's games; his best stretch was from September 24 through September 27, when he went 6-for-13 with two RBI over three games. He finished the year with a .224 batting average. After winning the National League East for the third consecutive year, the Phillies faced the Colorado Rockies in the National League Division Series, the Los Angeles Dodgers in the National League Championship Series, and the New York Yankees in the World Series; Bako did not appear in any games during the postseason. After the 2009 season, Bako filed for free agency; considered retirement, according to teammate Scott Eyre; and did not play during the 2010 season.