Gomez, the star of "Wizards of Waverly Place," won for TV actress, female hottie and music group with her band The Scene.
The 19-year-old performed at the ceremony in Los Angeles and took home a total of five wins - one more than boyfriend Justin Bieber.
Bieber, 17, picked up four surfboard-shaped trophies as choice male music artist, male hottie, twit and TV villain for his "CSI" guest starring role.
Other multiple winners included "The Vampire Diaries," "Glee," "The Twilight Saga," "Harry Potter and the Deathly Hallows," Robert Pattinson and Taylor Swift.
Swift tied Gomez with five awards. The 21-year-old singer was also honored for her contributions to entertainment with the Ultimate Choice Award, the show's version of a lifetime achievement award.
Past recipients of the annual honor include Justin Timberlake, Britney Spears, Reese Witherspoon and Sarah Michelle Gellar.
"The Big Bang Theory" star Kaley Cuoco hosted the 13th annual awards ceremony at Universal Studios Hollywood's Gibson Amphitheatre.
OneRepublic, will.i.am and Jason Derulo were among the musical performers.
The awards, which honor celebrities in TV, film, music and sports, are selected by online voters.
The Associated Press contributed to this report.