In the summer of 1983, Connor moved back to Celtic as new manager David Hay's assistant. He spent 2½ years in that role at Parkhead until he was sacked by Hay in February 1986. He then went to manage Raith Rovers from 1986 to 1990. Connor led Raith Rovers to promotion to the Scottish First Division in his first season in charge there, and succeeded in keeping them in that division for the remainder of his tenure as manager. After leaving Raith Rovers in 1990, Connor had a spell at Hearts as assistant to manager Joe Jordan.
In June 1993, Connor returned once again to Celtic, this time as part of Liam Brady's new backroom team. He was joined at Celtic by his former boss at Hearts, Joe Jordan.
In October 1993 following the departures of Brady and Jordan, Connor took over as caretaker manager of Celtic for four games. He was in charge for two Scottish Premier Division matches (one win, one draw) a UEFA Cup tie first leg (won 1-0 v. Sporting Lisbon), and he picked the team to face Rangers (a 2-1 Premier Division Celtic win) three days after Lou Macari's arrival. Connor had an unbeaten record in charge of Celtic.