"She broke up with him about a week ago," a source, whose name was not reported, told the magazine for a report published Saturday. "With them being apart so much it got complicated. She had some trust issues. It's not easy, but the relationship needed to end."
Bieber, 18, and Gomez, 20, made their relationship public in February 2011 after months of dating in secret.
Rumors swirled in August 2011 and again in July of this year that the two had broken up, People reported.
"I don't ever want her to feel like I'm ashamed of her," Bieber said of Gomez in an interview with Oprah Winfrey set to air Nov 25.