Branyan was placed on the disabled list on August 30, with a herniated disk in his back. He had stated that he had been bothered by lower back spasms throughout the season. He left the game against the Kansas City Royals after experiencing pain on a swing and underwent an MRI the next day. On September 27 the Mariners' manager Don Wakamatsu acknowledged it was unlikely that Branyan would be rejoining the Mariners in 2009. Branyan said on September 15 there might be a possibility of him playing before the end of the season. He was activated from the disabled list on September 30 but did not appear in any more games. However, the season still wound up being the best of his career. He finished 2009 with a .251 batting average, 31 home runs, 21 doubles, one triple, 108 hits, 224 total bases in 116 games. On the defensive side, he had a .990 fielding percentage with 10 errors (tied for most in the league for a first baseman) in 116 games at first base, all starts.