He became a tutor at Yale in June 1786, but, resigning this office, was ordained on November 9, 1786, and settled in Midway, Georgia,[3] where he remained until August of the following year.

He was very active in 1804 in the movement that resulted in enlarging the Massachusetts general assembly of Congregational ministers, and in 1805 unsuccessfully opposed, as a member of the board of overseers, the election of Henry Ware to the Hollis Chair of Divinity at Harvard.

[2] Morse did much toward securing the foundation of Andover Theological Seminary, especially by his successful efforts in preventing the establishment of a rival institution in West Newbury which had been projected by the Hopkinsians (chiefly Samuel Spring and Leonard Woods, with the financial backing of William Bartlett).

Morse rebutted certain racist views published in the Encyclopædia Britannica concerning the Native American peoples, e.g., that their women were "slavish" and that their skins and skulls were thicker than those of other humans.

[8] He took great interest in requiring Native Americans to become Christian, and in 1820 was appointed by the US secretary of war to visit and observe various tribes on the border in order to devise the most effective ways of assimilating them to European-American culture.

Beginning May 9, 1798, Morse delivered three sermons supporting John Robison's book Proofs of a Conspiracy, which first publicized the view that the Illuminati had masterminded the French Revolution.

The idea that I meant to convey, was, that I did not believe that the Lodges of Free Masons in this Country had, as Societies, endeavoured to propagate the diabolical tenets of the first, or pernicious principles of the latter (if they are susceptible of separation).

That Individuals of them may have done it, or that the founder, or instrument employed to found, the Democratic Societies in the United States, may have had these objects; and actually had a separation of the People from their Government in view, is too evident to be questioned.

[8] Morse published 25 sermons and addresses on special occasions; also A Compendious History of New England, with Elijah Harris (Charlestown, 1804); and Annals of the American Revolution (Hartford, 1824).