After leaving Arsenal, he made several appearances for Waltham Forest F.C., in the Ryman Division 1 North. He then joined the youth ranks at Cambridge United and after breaking into the first team he then moved to league club Northampton Town, where he signed on 16 May 2005. During his time at the club he was sent out on loan twice, playing for Gravesend & Northfleet and Stevenage Borough. Following the appointment of Stuart Gray as Northampton manager, Johnson featured in practically every single starting eleven that he named and he signed a new two-year contract extension.
Johnson began to attract attention from a host of Championship sides, including Coventry City, Colchester United and Queens Park Rangers, but was in talks to sign for Leicester City, after discussing terms at the Walkers Stadium on 2 January 2008. However, the player returned to the Sixfields Stadium, having failed to reach an agreement with the club.