While a 17-year-old senior at Jesuit High School of Tampa, Magadan was selected by the Boston Red Sox in the twelfth round of the 1980 Major League Baseball draft, but elected not to sign.

Following his breakthrough season at Alabama, Magadan was selected by the New York Mets with the 32nd overall pick of the 1983 Major League Baseball draft, early in the second round.

[6] Blocked at third base by Howard Johnson and at first by Keith Hernandez, Magadan still found his way into the lineup on a semi-regular basis in 1987 and 1988.

He provided a quality bat in late-inning situations and a capable spot starter whenever a regular needed a day off.

Magadan became the Mets' regular first baseman in 1989 when injuries limited Hernandez to 75 games and a .233 batting average.

[7] Marshall batted only .239 for the Mets, and had lost his starting job to Magadan by the time he was dealt to the Boston Red Sox on July 27.

The Mets once again went outside the organization to bring in a first baseman in the off season and brought in Eddie Murray, another former Dodger and eventual Hall of Famer, to fill the role.

He also became part of a historic moment on September 22, as the Mariners played host to the Texas Rangers inside the Kingdome.

Taking a pay cut, Magadan agreed to terms with the Houston Astros on a one-year deal for 1995.

Still, the Astros chose not to re-sign Magadan at the end of the 1995 season, choosing instead to acquire Sean Berry from the Montreal Expos to play third.

Injuries and a gold glove first baseman (Mark Grace) limited him to pinch hitting duties, and he batted only .254, and was used sparingly by manager Jim Riggleman.

[14] He made 328 plate appearances during the 1997 season, splitting his time fairly evenly between first, third, and designated hitter.

Magadan signed with the San Diego Padres in 1999 to back up first and third base, and subsequently re-signed with the team for the 2000 and 2001 seasons.

[18] In 2007, Boston would finally end their archrival New York Yankees' nine-year run as American League Eastern division champions, and went on to sweep the Colorado Rockies in the 2007 World Series.

[23] During the 2018 winter meetings in Las Vegas, Magadan was hired to be the hitting coach for the Colorado Rockies.