In 2002, Coyne was appointed pastor of Our Lady Help of Christians Parish in Newton, Massachusetts. His appointment raised controversy in the parish because Coyne had been the archdiocesan spokesman under Law, who had replaced a former pastor for speaking out against him. On February 1, 2003, after serving four months in Our Lady, Coyne requested a transfer to another parish from Archbishop Sean O'Malley. In 2006, O'Malley transferred Coyne to Saint Margaret Mary Parish in Westwood, Massachusetts
