In 1931, McIntire was ordained into the ministry of the Presbyterian Church USA, serving for two years at Chelsea Presbyterian Church, Atlantic City, New Jersey. In 1933, he was called to the Presbyterian Church of Collingswood, New Jersey, near Philadelphia, the largest church in the West Jersey Presbytery. McIntire remained a resident of Collingswood for the rest of his life. The Women's Missionary Society of the Collingswood church called his attention to what they perceived as a modernist perspective in the missions study book, which had been promoted by the denomination's Board of Foreign Missions. McIntire joined the conservative side in the ongoing Fundamentalist-Modernist debate, and in 1934, at Machen's invitation, he became a founding member of the Independent Board for Presbyterian Foreign Missions, an agency organized as an alternative to the denominational mission board that supported theologically liberal missionaries. Deeming the new board a challenge to its authority, the General Assembly demanded that the clergymen resign. After they refused, Machen, McIntire, and seven other clergymen were tried by an ecclesiastical court in 1935–36. The board members lost, and they renounced the jurisdiction of the Presbyterian Church, as did the Collingswood Presbyterian Church, only a tiny minority of whose members refused to support their young pastor.