In 2015 he coached in the Major Leagues on the Pittsburgh Pirates' staff, working under skipper Clint Hurdle.

After spending 1979 out of baseball, the 23-year-old Fischer was hired to manage the A's Short Season-A team in Medford, Oregon in 1980.

From 1985 to 1987, Fischer managed the Double-A Huntsville Stars to three playoff appearances and a Southern League championship, with the likes of José Canseco and Mark McGwire on his roster (albeit briefly).

At the conclusion of the 2007 season, the A's announced that he would not return, thus ending a 29-year relationship In 2008, he managed the State College Spikes, a Class A club affiliated with the Pittsburgh Pirates.

Released after the 2010 season, he was named field coordinator in the Pirates' player development department on December 22, 2010, until his promotion to Hurdle's 2015 staff.