McAteer got his big break aged 20, at local non-league team Marine, when impressing for Marine Reserves against the Bolton Wanderers A team in 1992. He had no contract with Marine, and Bolton purchased the young midfielder for £500 plus a large bag of footballs. He made his first team debut against Burnley in a Division Two game at Burnden Park on 28 November 1992, finishing on the winning side in a 4–0 triumph. He made a total of 21 appearances in the 1992–93 season for Bolton, who finished the season as runners-up and secured promotion to Division One. Bolton were FA Cup quarter-finalists in the 1993–94 season and achieved a comfortable position in Division One, but it was the 1994–95 season which proved most memorable, as Bolton reached the final of the Football League Cup (their first appearance in a major cup final for 37 years), but lost 2–1 to Liverpool.