Goldberg married actress Soleil Moon Frye (best known as the child actress who portrayed the title character on the 1980s TV sitcom Punky Brewster) on October 25, 1998. They wed in a traditional Jewish ceremony in Los Angeles. Their first child, daughter Poet Sienna Rose Goldberg, was born on August 24, 2005. Their second child, daughter Jagger Joseph Blue Goldberg, was born on March 17, 2008. Their third child, son Lyric Sonny Roads Goldberg, was born February 9, 2014. Their fourth child, son Story Goldberg, was born May 16, 2016.

Goldberg and Moon-Frye renewed their marriage vows in a ceremony in 2008. However, in 2020, after 22 years of marriage, the couple separated. The divorce was finalized in 2022.