Following his release by Scunthorpe United, Logan agreed a three-year contract to join Lincoln City in July 2000. He appeared in Lincoln's first five games of the 2000–01 season before sustaining an ankle injury in the 1–1 away draw with Hull City on 28 August 2000 which sidelined him for a month. Returning to fitness, Logan made a return as a substitute in the 2–0 home defeat to Mansfield Town on 30 September 2000 before suffering a prolapsed disc in his back. The injury required surgery and would keep Logan out of the first team picture for fourteen months.