He wrote a number of influential theological works, as well as hymns, essays and sermons, and edited two Universalist journals.

[2] Ballou preached at Barnard, Vermont, and surrounding towns in 1801–1807; at Portsmouth, New Hampshire, in 1807–1815; at Salem, Massachusetts, in 1815–1817; and, as pastor of the Second Universalist Church of Boston, from December 1817 until his death there.

Ballou, sometimes called an "Ultra Universalist," differed from Murray in that he divested Universalism of every trace of Calvinism, and opposed legalism and trinitarian views.

On this principle we contend, that the infernal torments, which false religion has placed in the future world, and which ministers have, with an overflowing zeal, so constantly held up to the people, and urged with all their learning and eloquence, have tended so to harden the hearts of the professors of this religion, that they have exercised, toward their fellow creatures, a spirit of enmity, which but too well corresponds with the relentless cruelty of their doctrine, and the wrath which they have imagined to exist in our heavenly Father.

By having such an example constantly before their eyes, they have become so transformed into its image, that, whenever they have had the power, they have actually executed a vengeance on men and women, which evinced that the cruelty of their doctrine had overcome the native kindness and compassion of the human heart.