Legal actions from the bishop's court made Morton decide to emigrate. He arrived in New England in July 1686 with his wife, his pupil, Samuel Penhallow, and his nephew, Charles Morton, M.D. Another nephew had preceded them in 1685. It had been proposed that Morton should become the principal of Harvard College, but another person was appointed before his arrival. He was, however, made a member of the corporation of the college and its first vice-president, and he drew up a system of logic and a compendium of physics, which were for many years two of its text-books. Lectures on philosophy which he read in his own rooms were attended by several students from the college, and one or two discontented scholars desired to become inmates of his house, but these proceedings gave offence to the governing body. Morton was also inducted as minister of the first church in Charlestown, New England, on 5 November 1686, and was the first clergyman of the town who solemnised marriages. He was prosecuted for alleged seditious expressions in a sermon preached on 2 September 1687, but was acquitted. His name is the second of the petitioners to the council on 2 October 1693 for some encouragement to a system of propagating Christianity among the Native Americans, and his was the senior signature to an association for mutual assistance among the ministers of New England. He acted with those who urged the prosecutions for witchcraft at Salem, Massachusetts.