He was snapped up by Hereford United of the Conference, where he was second choice goalkeeper to Scott Cooksey in the 2000–01 season, although he started two league matches conceding a goal in each.
However a serious wrist injury forced Cooksey onto the sidelines, and eventually into retirement, meaning Baker started the 2001–02 season as first choice keeper where he impressed.
Most notably he had an inspired Man-of-the-Match performance in the FA Cup against future club Wrexham, a match which was televised live by the BBC, as Hereford won 1–0.
However, he spent only six months at the Racecourse Ground before signing for MK Dons, for whom he quickly became a fans favourite, and helped them survive relegation in his first season, and went on to make over 60 first team appearances.
On 20 July he joined Macclesfield Town on trial but despite again impressing was forced to retire from the game in August 2007 due to a reoccurrence of a knee injury.