Stein retired from professional footballer in 1992 to become manager at former club Barnet; at the time he was just one of two black managers in the country, alongside Keith Alexander. Stein resigned from Barnet in July 1993 in order to become Assistant Manager at Southend United, under former colleague Barry Fry. He later became manager of non-league side Harrow Borough, leaving that position in November 2003 after three-and-a-half years.
Stein took over as manager of Southern Premier Division side Banbury United in September 2012. He resigned in August 2014.