In 1844 John, returned to Liverpool as Fr. Murphy, and was inducted as priest-in-charge to the newly formed parish of St. Joseph's in the Irish quarter of the city. The famine in Ireland had already caused many of the Irish to seek refuge in Liverpool, where famine fever raged among the Irish residents. With his own money Fr. Murphy purchased a Methodist Chapel in the district, which he converted into a Catholic church. For three years he ministered to the spiritual and physical needs of his fellow Irish men and women.