Allen was born in 1596. It is believed he was of Christ's College, Cambridge at the University of Cambridge, where he proceeded M.A. According to the Dictionary of National Biography, he is described "by one not given to laudation" as having been ‘a hard student, a good scholar,’ and it is added he was ‘an excellent preacher, a grave and pious divine, and a man of a most humble, heavenly, and courteous behaviour, full of sweet christian love to all.’ Nonetheless was he exposed to the politico-religious persecutions of the times. Being ‘settled’ at Ipswich, he came under the ban of Bishop Wren. He voluntarily left his ‘cure’ and removed to London, rather than be contentious.
To America
About the year 1637–8 he accompanied a band of English Puritanism to New England, ‘being obliged to goon board the ship which was to convey him thither in disguise, in order to elude pursuit.’ He was invited by the residents to settle in Dedham, Massachusetts "with thoughts of future employment in publik worke." In 1639 he was chosen pastor of the First Church and Parish in Dedham where he continued "much beloved and useful all the rest of his days," only now and again accompanying Eliot in his "labours" among the Indians.
Nine Positions
In 1637 a number of English divines, having had it bruited that their brethren in New England were departing from the old landmarks in regard to ecclesiastical discipline and order, addressed to them a letter of inquiry in respect to what they called the ‘Nine Positions.’ The New-England divines answered the communication at great length, frankly acknowledging that on certain points their views had been modified. This in turn was replied to by John Ball on behalf of the English divines, and to this finally a very able and pungent answer was given by Allen along with Thomas Shepard, entitled ‘A Defence of the Nine Positions.’
Baptism controversy
Later, a protracted controversy agitated New England on the proper ‘subjects’ of baptism. Allen was foremost in the fray, and published a vigorous ‘Defence of the Synod held at Boston in the year 1662.’ He was likewise associated with Shepard in a treatise on ‘Church Reformation.’
Limitation of colonial allegiance
But Allen was more than a pastor and preacher. Though of rare patience and peacefulness, he could take a stand when called to it. Necessity was laid on him to do so very strongly and peremptorily. In 1646 an attempt which was made to bring the colonists into subjection to the British parliament produced passionate resistance. Allen was chosen to be the ‘voice’ of the colony, and he submitted a statesmanlike paper in ‘a manly and decided tone,’ marking the just limitations of colonial allegiance and imperial rights, and fully sustaining the colonists.
Personal life
He was twice married. His first wife, Margaret, went over with him to New England. Shortly after her death he married his second wife Katharine, widow of Governor Thomas Dudley. He left three sons, and all over the United States to-day families are found to trace their descent from him. He died on 26 August 1671. He is buried in the Old Village Cemetery. His bereaved congregation published his last two sermons: the one from Song of Solomon viii. 5, and the other from St. John xiv. 22. In their preface the editors denominate him ‘a constant, faithful, diligent steward in the house of God, a man of peace and truth, and a burning and shining light.’ These two sermons were some years since reprinted in a memorial volume, entitled The Dedham Pulpit.