It first met secretly in members homes, and the doors of the first church were nailed shut by a decree from the Puritans in March 1680.

The church was forced to be disguised as a tavern and members traveled by water to worship.

Shortly before the founding of the church, the first Harvard College president, Henry Dunster, was forced to resign his position for refusing to baptize his infant.

Dunster had been theologically influenced by Dr. John Clarke and other Rhode Island Baptists persecuted in Massachusetts.

[2][4] The current church building (fifth meeting house) was designed by the notable architect Henry Hobson Richardson and built in 1869–71.

The historic and prominent tower with distinctive friezes carved "in-situ" by Frédéric Auguste Bartholdi (sculptor of the Statue of Liberty) representing four sacraments, with faces of famous Bostonians (including Longfellow and Hawthorne), Abraham Lincoln, and Bartholdi's friends of that era, (including Garibaldi).