Harvey suffered a heart attack before a league match against Cambridge United in November 2005. Whilst Harvey was given time off to recuperate, McIlroy was installed as caretaker manager. McIlroy took Morecambe into the play-offs during Harvey's absence, and on Harvey's first day back after his illness in May 2006, he was sacked with McIlroy being installed as permanent manager in his place. Harvey's sacking from Morecambe has led to serious animosity between the two former friends and colleagues; they refused to shake hands when Harvey's Forest Green side met McIlroy's Morecambe at Christie Park in November 2006.
After spending the pre-season coaching at Crewe Alexandra, in September 2008, Harvey replaced Gary Owers to become Forest Green Rovers' seventh manager in nine seasons. He took over a team bottom of Conference the with just 2 points from the first six games and led them to safety with a game to spare. In his second season as Forest Green boss he led the club to its highest ever league finish of 8th in the Conference National under his guidance. He then led the club to the third round of the FA Cup in his third season at Forest Green where they narrowly lost 4–3 to Championship side Derby County. In the same season he took Forest Green into the Conference League Cup Final following a 1–0 away win at Ebbsfleet United in the semi finals however Forest Green lost in the final to AFC Telford United 0–3 on penalties after the game finished goalless. He left the club in August 2009.
On 6 October 2009, Harvey was appointed manager of Chester City until the end of the 2009–10 season, where he had previously been part of the coaching staff in the mid-1990s. However Harvey resigned in January 2010 because of uncertainty regarding his future. On 12 February 2010 Harvey was appointed manager of Stalybridge Celtic in the Conference North. He left the club in October 2013.