Bako appeared in 73 games for the 1999 Astros; he got at least one hit in his first six games with Houston after beginning the season in the minor leagues, highlighted by a 3-for-4 performance on April 30, the anniversary of his debut. He added another 4-for-4 game to his résumé on July 29 against the Colorado Rockies. Bako hit .256 with two home runs, 17 RBIs, and 16 runs scored in the 1999 season; he was part of Houston's roster for the 1999 National League Division Series, but did not play. After one game for the Astros in 2000, Houston traded Bako to the Florida Marlins. He played his first game for Florida on April 13, going 0-for-4 with a strikeout. Bako played for the Marlins until July 20, batting .242 with 14 RBIs. He was waived on July 21 and claimed by the Atlanta Braves, one of the Marlins' division rivals. He batted .190 with the Braves and played in his first career game at first base in the last two months of the 2000 season.