The Universalists survived the Restorationist controversy and compensated in 1833 by creating a central ecclesiastical body, the United States Convention of Universalists. That same year, the Unitarians faced telling evidence of an organizational vacuum when the Standing Order of Massachusetts was disestablished. A lack of centralized authority, coupled with an insistence on freedom of conscience, meant the two churches – Universalist and Unitarian – would find themselves in the ensuing decades riddled with conflict over relationships to revelation, miracles, scientific truth, and ultimately Christianity itself.

Nothing is more celebrated in American Unitarian history than the revolt of the younger generation of Transcendentalists from their Unitarian parents. Agitated for religious reasons, they longed for a direct and immediate relationship with God, as experienced through nature. Even before the publication of his essay Nature in 1836, Ralph Waldo Emerson (1803–1882) had rejected the rational “corpse cold Unitarianism of Brattle Street and Harvard College” for a “return to reason and faith.” In the spring of 1827, Emerson found himself torn between the family profession of parish ministry modeled by his father, and the poetic muse of “feeling” inspired in him by his Aunt Mary Moody Emerson. Emerson chose ministry, but soon gave up the social world of his father, his attachment to Christianity, and his formal affiliation with the church. His public reasons for the resignation were explored in his essay, The Lord's Supper. Emerson argued, “Jesus did not intend to establish an institution for perpetual observance.”