During the late 1920s, Princeton Seminary was embroiled in the Fundamentalist-Modernist Controversy that had disquieted the Presbyterian Church in the United States of America as well as other Protestant denominations. McIntire became a strong supporter of J. Gresham Machen, a conservative professor of New Testament. With Machen, McIntire opposed a reorganization of the seminary in 1929 that appeared to strengthen liberal elements in the church. He followed his mentor and three other professors from Princeton to the newly founded Westminster Theological Seminary, where he completed his Th.B. degree in 1931.