That year Breckinridge accepted the call to pastor the Second Presbyterian Church of Baltimore, Maryland. While at the church, he became involved in a number of theological debates. During the Old School-New School Controversy within the Presbyterian Church in the 1830s, Breckinridge became a hard-line member of the Old School faction, and played an influential role in the ejection of several churches in 1837. He was rewarded for his stances by being elected moderator of the Presbyterian Church's General Assembly in 1841.