On June 13, 1984, Carter was traded with three other players to the Cleveland Indians for Rick Sutcliffe, George Frazier, and Ron Hassey.

After a strong 1989 season, Carter was traded by Cleveland to the San Diego Padres for prospects Sandy Alomar Jr., Carlos Baerga, and Chris James.

The Padres subsequently dealt him to the Toronto Blue Jays along with Roberto Alomar in exchange for star players Fred McGriff and Tony Fernández.

Carter's overall game improved dramatically in 1991, as he helped the Toronto Blue Jays win the division title and hit the game-winning single that clinched the AL East championship; he also emerged for the first time as a team leader.

Carter hit two home runs and recorded the final out of the Series, taking a throw to first base from reliever Mike Timlin to nab Otis Nixon of the Atlanta Braves, who bunted.

Tom Cheek, the Blue Jays' radio broadcaster, called the play: "Touch 'em all, Joe, you'll never hit a bigger home run in your life!

[11] In 1993, while a Toronto Blue Jay, Carter set an American League record when he hit 3 home runs in a game for the fifth time in his career.

From 1999 to 2000, Carter served as a color commentator for the Toronto Blue Jays on CTV Sportsnet, leaving to work for the Chicago Cubs.

From 2001 to 2002, Carter served as the color commentator, alongside play-by-play man Chip Caray, for the Chicago Cubs on WGN-TV.

On August 7, 2009, Carter, along with many of his 1992 and 1993 Toronto Blue Jay World Series alumni teammates, attended a reunion/pre-game ceremony at the SkyDome.

The event was organized by Carter himself and included three dozen players, coaches and athletic trainers from the Blue Jays' 1992 and 1993 World Series rosters.