It was founded in order to promote Congregationalism and was also an important voice in support of abolitionism and women's suffrage.

From its founding in 1848 until 1861 The Independent was edited by a team of three prominent Congregational ministers: Joseph Parrish Thompson, Richard Salter Storrs, and Leonard Bacon.

The editorial policy was strongly antislavery, which hurt the magazine's circulation initially, but it improved through the 1850s to reach 35,000 by the beginning of the American Civil War.

It also published poetry and literary contributions by authors including Elizabeth Barrett Browning, Harriet Beecher Stowe, Emma Lazarus, John Greenleaf Whittier, James Russell Lowell and Edward Eggleston, who was also briefly supervising editor, in 1871.

During the second decade of the twentieth century The Independent absorbed three other magazines: The Chautauquan (1914), Harper's Weekly (1916), and Countryside (1917).