In 2006, Bowden scored her first acting role in a two-episode arc on the ABC long-time running daytime soap opera television series One Life to Live as Britney. She has since guest starred on shows such as Law & Order: SVU and Ugly Betty. Bowden's breakthrough role came when she was cast as a recurring character on the Emmy Award winning Comedy television series 30 Rock, which premiered on October 11, 2006 on NBC. She portrayed the sexy but incompetent assistant Cerie. She signed on as a regular for the show's second season in 2007. The show's final episode aired in January 2013, in total consisting of 7 seasons. She appears in the music videos "Dance, Dance" by American rock band Fall Out Boy, as well as "After Hours" by Brooklyn band We Are Scientists.
In April 2011, Bowden was voted as Esquire Magazine's Sexiest Woman Alive. She was also the face of the Jordache television campaign that made its premiere in September 2011. In April 2011, Universal Pictures announced that Bowden was cast as the role of Mia, an "L.A. party girl type", and girlfriend to Chris Klein's character, in the fourth installment of the American Pie film trilogy, American Reunion. The film was released on April 5, 2012 to mixed reviews but financial success. Also in 2012, Bowden appeared in Piranha 3DD, which was panned by critics and the horror movie Hold Your Breath which received a limited theatrical release before being released to DVD.
On January 28, 2012, Bowden got engaged to her boyfriend of nearly two years, musician Ben Jorgensen from the band Armor for Sleep. They were wed May 19, 2013 in the Brooklyn Botanical Garden in New York.