Bako's 1995 performance earned him a promotion to the Southern League's Chattanooga Lookouts, the Reds AA-level affiliate, for 1996, where he was named a Southern League All-Star. He was second on the team in strikeouts (93) and fifth among regulars with a .294 batting average. He hit a career-high eight home runs during that season, adding 27 doubles and 48 RBIs in 360 at bats. In 1997, playing for the Indianapolis Indians, Bako was a teammate of brothers Aaron and Bret Boone. That year, he batted .243 and matched his previous year's career-high home run total. He had 78 hits in 321 at-bats. Bako's game management earned him a reputation, even in the minor leagues. Brett Tomko, who played with Bako in the minors in 1996 as a member of the Lookouts and in 1997 with Indianapolis, recalled one of their mound conversations: