Morgan became Sheffield United's reserve team coach shortly after sustaining a serious knee injury in October 2010. During the 2011–12 season, while still a registered player but unable to play due to injury, he led United's reserves to the Central League title. In April 2013, Morgan was appointed as caretaker-manager for the remainder of the 2012–13 season after the departure of manager Danny Wilson. Despite United winning Morgan's first game in charge, results did not significantly improve and they failed to clinch promotion, losing to Yeovil Town in the semi-final of the League One play-offs. Despite publicly expressing his desire to take on the role on a permanent basis, Morgan was overlooked for the post of full-time manager in favour of former Scotland defender David Weir. Weir's brief reign was ended on 11 October, at which point Morgan resumed his role as caretaker-manager. He worked as first team coach under new boss Nigel Clough, before going on to coach the under-21 side after Nigel Adkins took charge in the summer of 2015. On 30 December 2015, Sheffield United announced that they had "reluctantly" released Morgan, and that he would be joining Chesterfield as first team coach under manager Danny Wilson. Wilson and Morgan were sacked in January 2017. He joined the coaching staff at Port Vale two months later, where former teammate Michael Brown was caretaker-manager. On 16 September, Brown was sacked following seven games without a win, and Morgan and David Kelly were installed as caretaker-managers. The duo took charge of four games, before both men left the club once Neil Aspin was appointed on 4 October. Morgan was appointed as inaugural Chairman of the Sheffield United Former Players' Association in November 2015. In February 2018, Morgan joined high-profile agency Stellar Group to work as a football intermediary.