During the 1800 election, accusations were made against Jefferson’s faith—along the lines that he was a skeptic. He did not agree with what he was being accused and responded on occasion.
Jefferson replied to New Hampshire politician and minister, Rev. William Plumer, on January 31, 1815, saying, “. . . with those to whom it is addressed [i.e. northeastern clergy] Moses and the prophets have no authority but when administering to their worldly gain; . . . anyone who perverts the sanctity of his desk [i.e. pulpit]. . . .”
Jefferson replied to Peter Wendover on March 13, 1815, with a short version that simply said “. . . the Eastern clergy have not deserved well either of their religion or their country. . . .” But a longer unsent version mentioned “. . . the Robespierres of the priesthood. . . .” Robespierre, of course, was the notorious French Revolutionary, who in the Jacobin “reign of terror,” imposed his views in the name of the Deist Supreme Being. This description does not support the image of Jefferson as a French-minded Deist. Rather he connects that with the clergy of New England.
On August 6, 1816, Jefferson wrote Margaret Bayard Smith (also known as Mrs. Samuel Harrison Smith) saying: “. . . the [northeastern] priests indeed have heretofore thought proper to ascribe to me religious, or rather anti-religious sentiments, of their own fabric. . . .”
In 1817 on the same day, May 5, that Jefferson met Rev. John Goss, also a magistrate in Charlottesville, he wrote to John Adams: “. . . I join you therefore in sincere congratulations that this den of the priesthood [i.e. an official state Congregational church in Connecticut] is at length broken up, and that a protestant popedom is no longer to disgrace the American history and character. . . .”
On November 4, 1820 he writes to Unitarian Rev. Jared Sparks, saying: “. . . perverted by His pseudo priests. . . .”
On March 6, 1822, Rev. Jedidiah Morse of New England, asked him to join a new national society but Jefferson declined saying, “. . . in the society . . . ; the clergy will constitute nineteen twentieths of this association . . . ; we are to guard against ourselves. . . .”
We see overall a repeated pattern of Jefferson’s antipathy toward abuse of power by priests. The majority of cases cited, whether in Europe or even in the northern states of America, were those in which priests were leaders of a church-state system. On the other hand, we see Jefferson enjoying relationships with Christian dissenters. Jefferson’s antipathy was toward the abuse of power, even if it was (especially if it was) in the name of God.
While he maintained friendly relations with many clergy, especially dissenters, including Presbyterians, for the bulk of his life, there arose a conflict between him and Presbyterians in 1820. That was the exception not the norm in his long life.
 Letter to William Plumer, January 31, 1815. Papers, Retirement Series, vol. 8, 229.
 Letter to Peter H. Wendover, March 13, 1815. Papers, Retirement Series, vol. 8, 340.
 Letter to Margaret Bayard Smith, August 6, 1816.
 Letter to John Adams, May 5, 1817. Bergh, Writings, vol 15, 108–111.
 Letter to Rev. Jared Sparks, November 4, 1820. Dickinson Adams, 401.
 Letter to Rev. Jedidiah Morse, March 6, 1822. Ford, The Works, vol. 12.