As the congregation at Stone Chapel wished to remain connected with the Episcopal Church, in 1786 they sent a request to Bishop Samuel Seabury to have Freeman ordained as their rector. Because of the controversy surrounding the changes that had been made to Stone Chapel's liturgy, Seabury replied that he would require the recommendation of his presbyters. After interviewing Freeman and confirming that he did not subscribe to the Trinity, the presbyters denied his application for ordination. A more liberal-minded clergyman, Samuel Provoost, bishop-elect of New York, also declined his support. The wardens of the church then took it upon themselves to arrange a lay ordination. In 1787 Freeman was made "Rector, Minister, Priest, Pastor, and Ruling Elder" of Stone Chapel.