After his resignation, Pierpont served as pastor of a Unitarian church in Troy, New York (1845–1849), and then led the First Parish Church (Unitarian) in Medford, Massachusetts (1849–1856).
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He ran for Massachusetts governor during the 1840s as a Liberty Party candidate, and in 1850 as a Free Soil Party candidate for the US House of Representatives.
The poem titled The Airs of Palestine was first published by John Pierpont (1785–1866) in 1816 (Baltimore: B. Edes; various reprints).
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