On February 1, 2008, Bako signed a minor league contract with an invitation to spring training with the Cincinnati Reds. At the end of spring training, he was added to the 40-man roster. Though he batted only .217, Bako appeared in a career-high 99 games in 2008, hitting six home runs and notching 35 RBIs. On January 30, 2009, the Chicago Cubs signed Bako to a one-year contract. However, he was unconditionally released near the end of spring training. On May 18, Bako signed a minor league deal with the Philadelphia Phillies, and was called up from the Reading Phillies to the Major League roster on June 9. He became the Phillies only backup catcher when the Phillies waived "folk hero" Chris Coste on July 10; Coste had broken into the big leagues for the first time with Philadelphia at age 33. The next day, Bako came to the plate in the bottom of the ninth inning against Pittsburgh Pirates closer Matt Capps with the score tied, 7–7; the Phillies had been behind by four runs before home runs by Matt Stairs and Ryan Howard tied the game. With the bases loaded, Bako hit a single through the left side of the infield, driving in the winning run (Raúl Ibañez) and sealing the Phillies fourth consecutive victory in a season-high ten-game winning streak. After the acquisition of starting pitcher Cliff Lee, Bako caught all of his first five starts with the Phillies, when Lee posted a 5–0 record and an 0.68 earned run average. Bako said, "With as many strikes as he throws and as many weapons as he has, it's a lot of fun to catch him." Manager Charlie Manuel, however, denied that Bako was scheduled to be Lee's personal catcher, as he had done for Maddux in 2001. "'s not his personal catcher... Of course you guys will write whatever you want to write. If you want him to be his personal catcher, go right ahead. But I'll handle it anyway, so it doesn't matter."