Scott played his first professional season with their rookie league Gulf Coast Yankees in 1981, and his last with Oakland's Triple-A Tacoma Rainiers in 1990.

Since retiring from the field, Scott has been a minor league manager for the Athletics and Arizona Diamondbacks, a scout for the Diamondbacks, player development director of the Toronto Blue Jays, and field coordinator of instruction for the Houston Astros and New York Mets.

He also served as Director of Player Development for the Mets[1] under Sandy Alderson, for whom Scott had previously worked in the Oakland organization.

On December 16, 2015, Scott was announced as the new bench coach of the Mets, succeeding Bob Geren.

[2] He served in the position through the 2016 and 2017 seasons before leaving the Mets to become player development director for the Miami Marlins.