Coaching and management career
John Connolly was appointed manager of Dumfries club Queen of the South in July 2000 and appointed Scott as his assistant manager. Under the captaincy of Jim Thomson and Andy Aitken, another defensive mainstay, Connolly and Scott led the club to the Scottish Second Division Championship in the 2001-02 season. They clinched the title on 20 April 2002 with a 3–0 away win versus Forfar Athletic. This was Queens first league championship since Jimmy McKinnell Junior led the club to the Division B Championship in the 1950-51 season.
The following season Queens won the 2002-03 Scottish Challenge Cup, defeating Brechin City 2–0 in the final at Clyde's Broadwood Stadium. Robbie Neilson and Andy Goram were in the starting line-up for Queens that particular day, beside captain Thomson.
When Connolly left Dumfries in 2004, Scott was appointed Queens manager in his place. As an Englishman, he became the first non-Scot to manage Queens. He guided them to 4th in the league table, at the end of his first full season in charge.
He has since been involved in coaching with Gretna alongside Mick Wadsworth and Andy Smith, following which he joined the SFA coaching team, responsible for development and coaching in the Aberdeen region.
in his first season as coach in 2011 Scott lead Seacoast United Phantoms to the North East Professional Development League title (PDL) USA.
In 2014 Scott secured his second title in four years with the Phantoms by winning the Professional Development league(PDL) again with only one defeat during the regular season and his team led the country with goals against.