Ellis then had a brief spell as manager of Bury before moving to Manchester City as Peter Reid's assistant manager. In 1994, he was appointed manager of Lincoln City before returning to Gigg Lane as Stan Ternent's assistant the following year. When Ternent moved to Burnley in 1998, Ellis followed him. After six years at Turf Moor, Ellis became assistant manager to Kevin Blackwell at Leeds United for 2 years. Ellis later worked with Blackwell at Luton Town (after a spell at Stoke City) and Sheffield United.