Roberts had his daughter Emma Roberts on February 10, 1991 with his then-girlfriend Kelly Cunningham. The relationship ended. Then, he married Eliza Garrett in 1992. His daughter Emma has joined her father and aunts in the acting business. She has a starring role on the Nickelodeon series Unfabulous and has appeared in the films Blow (2001), Aquamarine (2006) and starred in Nancy Drew (2007) as the title character.

On January 12, 2001, Roberts visited The Howard Stern Radio Show with his wife during a segment called "The Gossip Game" with Mike Walker of the National Enquirer on the telephone and shared a bit of personal information. He confirmed that he and his more famous sister Julia Roberts were estranged for several years. The source of the estrangment had been Eric's past drug abuse, and Julia's siding with his ex-girlfriend over the custody battle over Emma Roberts. In 2004, he told People magazine, that he and Julia reconciled when he went to visit her in the hospital a