Daulton missed nearly the entire 1996 season due to injury; he played in only five games, all as an outfielder. In 1997, he returned to the outfield in an attempt to keep his still-productive bat in the line-up, despite his chronic injuries. Daulton also played 42 games as a first baseman.
On July 21, 1997, after 17 years with the Phillies organization, the club traded Daulton to the Florida Marlins for Billy McMillon. By that time, Daulton's knee injuries had escalated even further, limiting his usage to playing first base and pinch hitting. He ended the 1997 campaign with a .263 batting average, 14 home runs, 63 RBI, and 68 runs scored, in 395 at bats. Daulton batted 7-for-18 (.389) in the 1997 World Series, as the Marlins defeated the Cleveland Indians. Daulton announced his retirement, after the series.