Trott's separation from the Methodists was inevitable. He realized that his disagreements with the denomination extended far beyond questions about the proper subject and mode of baptism. In the spring of 1832, he wrote a letter to a Mr. McLeod, the Methodist Superintendent of Cherokee Missions. Trott stated that in addition to the practice of sprinkling infants, he had come to reject the authority of all human creeds and the denominational habit of treating human opinions as though they were matters of revealed faith. In particular, he renounced the notion, spelled out in the Methodist book of discipline, that the Lord expected him to adhere to John Wesley's creeds as his standard for teaching. He also rejected the polity of the Methodist Church with its four orders of bishops and five kinds of tribunals. He concluded his letter by describing his predicament:
Thus, you see, I am compelled to refrain from preaching what I believe to be the truth, to preach what I cannot believe, to suffer expulsion, or to withdraw. I prefer the latter.From then on, Trott considered himself a mere Christian and identified himself as part of the movement that Alexander Campbell called "the present reformation."
But this change did not dampen his commitment to making disciples among the Cherokee Indians. As noted in the previous post, in the early 1830s, the State of Georgia had brutally persecuted Trott, along with dozens of other missionaries, because he refused to take an oath of loyalty to the state which denied all Indian land claims. Still, according to the Cherokee Census Roll of 1835, he was then still residing in Georgia. According to the census, he lived near Oothcaloga Creek where he owned a mill. The record further indicates that Trott, whose first wife died in 1830, had since remarried, and that the two children from the first marriage were living with him.
 Tolbert Fanning, "James J. Trott: Messenger of the Church of Christ at Franklin College, Tenn., to the Cherokee Nation," Gospel Advocate 11 (March 25, 1869), 271-73.
 James J. Trott, Letter to Alexander Campbell, Millennial Harbinger 3, no. 8 (August 6, 1832), 389.
 Ibid., 389-90.
 Copies of Manuscripts in the Office of the Superintendent for the Five Civilized Tribes, Muskogee, Oklahoma: Cherokee Census Roll of 1835, Compiled from Original Record selected by Grant Foreman, 14: 224. The entire entry for James J. Trott reads as follows: "Three Cherokees, 1 white marriage; 2 readers of English, they owned a mill; one weaver, 1 spinster, 2 descendants of reservees."