The "Loser" singer filed the documents on Friday afternoon, the day after Valentine's Day. The couple was married in 2004 and they have two children together, 14-year-old son and an 11-year-old daughter.
The couple are both Scientologists, as is her twin brother, actor Giovanni Ribisi.
Earlier this week, Beck released a song called "Super Cool" for the soundtrack of "The Lego Movie 2: The Second Part."
Beck has won seven Grammys in his career, including Album of the Year in 2015 for "Morning Phase." He won two at this year's awards: Best Alternative Music Album and Best Engineered Album, Non-Classical.