In 1898 the American Unitarian Association elected him secretary (a position effectively the chief executive officer) but in 1900 the position was redesignated as president and Eliot served in that office from inception to 1927, significantly expanding the association's activities and consolidating denominational power in its administration.

He enrolled at Harvard Divinity School the following year, and after briefly serving as a missionary in Seattle, Washington, graduated in 1889.

[1] Eliot left congregational ministry to serve as Secretary of the American Unitarian Association (AUA) in 1898.

Responding to declining wealth in American central cities in the early twentieth century, Eliot encouraged the growth of suburban Unitarian churches.

[1] He was also active in shaping the political commitments and demographics of Unitarian clergy by using his office to de-fellowship ministers who objected to American involvement in World War I, discouraging women from seeking Unitarian ordination, and excluding women ministers from associational leadership.