Breckinridge served as a Ruling Elder at the Presbyterian General Assembly of 1832, then relocated to Princeton, New Jersey, to study under Samuel Miller at Princeton Theological Seminary. In November 1832, he succeeded his brother John as pastor of Second Presbyterian Church of Baltimore, Maryland. His tenure saw numerous converts, but he was put at odds with his brother and Samuel Miller over practices employed in his church. His counselors were also concerned that he was wavering on his belief in the doctrine of limited atonement. Eventually, he was persuaded back into the doctrines of the orthodox Calvinism and became one of the leaders of the Old School Presbyterian movement.