In 1983, Metcalf married Jeff Perry, co-founding member of Steppenwolf Theatre Company; the two had a daughter, Zoe Perry, 1983. They divorced in 1986.
Metcalf later began a relationship with Matt Roth, the Roseanne co-star who played her abusive boyfriend Fisher. By November 1993, they had a son, Will, and eventually married. They also worked together on occasion, including in the 1994 feature film thriller Blink and the 1998 drama Chicago Cab; they also appeared together in an episode of Desperate Housewives.
Their daughter, Mae Akins, was born in 2005 via surrogate. They had a second son, Donovan, whom they fostered at six years old in 2006 and later adopted.