Arroyo was diagnosed with carpal tunnel syndrome in his pitching hand during the 2008–09 offseason. As a result, he missed games during the 2009 spring training, as well as being advised to stop playing guitar until the symptoms disappeared. After a sub-par first half of the 2009 season, Arroyo turned in an excellent second half, lowering his ERA from the 5's to the 3's, throwing multiple shutouts and complete games, and putting himself in position to be the Reds top starter in 2010 since Edinson Vólquez, the #1 starter in 2009, was out for the start of the season following Tommy John surgery. Arroyo finished the 2009 year with 2 shutouts, a 15–13 record, and a 3.84 ERA.
In 2010, Arroyo was chosen as the #2 starter in the Reds' first playoff series in 15 years. He pitched 5 ⁄3 innings against the Philadelphia Phillies, allowing one earned run and leaving with the lead. However, he would earn a no-decision as the Reds went on to lose the game. Arroyo won his first Gold Glove on November 10, 2010, the first by a Reds pitcher since Harvey Haddix in 1958. He finished the 2010 year 17-10 and a 3.88 ERA.
The Reds exercised the 2011 option on Arroyo's contract on November 3, 2010. After exercising his option, the Reds and Arroyo agreed on a three-year, $35 million contract extension, keeping him with the team through 2013.