 After his term as President of the Methodist Conference, Thompson was involved with the sacramental controversy of the early 1790s.His pen drafted the Plan of Pacification of 1795, which arose out of disputes between the Methodist societies and the Church of England over the status of travelling preachers and the administration of the sacraments, fomenting their separation.He was serving as Chairman of the Birmingham District when he died on May 1, 1799.