He retired from the legislature in 1999 and returned to his position as rector of St. Clement's (Riverdale) Anglican Church. In 2000, Shea initiated and was later elected founding chair of the Ontario Association of Former Parliamentarians. In 1999 Shea was inducted as rector of St Hilda's parish in Toronto and Chairman and CEO of St Hilda's Towers, a 500-bed independent and assisted living seniors residence including extended convalescent care facilities. In 2002 he was installed as a canon in the Diocese of Toronto.