In 1999, Tilson returned to Southend United as Director of the club's new centre of excellence, the establishment of which was made possible by a grant of £276,000 from the English Sports Council. The post, which enabled him to continue his playing career with Canvey Island, saw him responsible for overseeing and developing all of the centre's teams, raging from the under-9 to 16. Following the departure of David Webb as Southend United's manager in October 2001 and the promotion of Rob Newman from reserve team manager to first team manager, Tilson's role widened to take on Newman's previous duties with the reserve team. In May 2002, he drew time on his five-year career with Canvey Island to join Newman's backroom team on a full-time basis becoming joint assistant manager with Blues' former striker David Crown.