The first colonists living in what was then called "Mystic Side" attended the church in Charlestown, which forced the settlers to make a long journey, including taking a ferry.

Matthews had been preaching in Hull, Massachusetts but had lost the favor of the freemen there, and thus his ordination in Malden was opposed by the other churches and by the magistrates of the General Court.

[4] As a result of this conflict with neighboring churches, the historical record suggests that Matthews was lay-ordained, instead of ordained by the elder Charlestown congregation as was customary.

The second ordained minister to preach in Malden was Michael Wigglesworth, a preacher and poet who was renknowned for his scriptural poem The Day of Doom.

In 2009 the church voted to become LGBT affirming and were joined by Tonya McCloskey and Marcia Kadish, the first same sex couple to marry in Massachusetts.