Affeldt returned to Kansas City's starting rotation in 2006 when he was named the fourth starter during Spring training. However, he was moved up to the third spot before the season began when Runelvys Hernández was demoted to the fifth spot. Affeldt struggled as a starter, going 2–5 with a 7.80 ERA in nine starts. His final major league start came on May 27 against the New York Yankees. He gave up ten runs on eleven hits in a 15–4 loss. After the start, he was sent to the bullpen, and Bobby Keppel filled his place in the starting rotation. Affeldt improved in the bullpen, posting a 2.91 ERA there through July 31.