As vicar general, Monsignor Duffy was instrumental in the establishment of Queen of Angels, the first parish for people of color in the Newark diocese.

[3] He was the diocese's apostolic administrator between the death of John O'Connor and the appointment of Thomas Walsh, and served as pastor of St. Joseph's Parish in Jersey City.

He received his episcopal consecration on June 29, 1933, from Archbishop Walsh, with Bishops James Griffin and Alphonse Smith serving as co-consecrators.

[7] During his tenure, he established the Diocesan Fund for the Faith for those left in need because of the Great Depression, erected parishes in the sparsely settled areas of the diocese, and organized the Catholic Youth Organization, Bishop's Committee for Christian Home and Family, Confraternity of Christian Doctrine, and Newman Clubs.

[8] John Duffy died on September 27, 1944, at age 59, and was buried next to his parents in Holy Name Cemetery in Jersey City.