On 10 November 1653 Edmund and two others received presbyterian ordination at Moreton, Essex, of which Samuel Hoard (not one of the five ordainers) was rector.
Hoard died in February 1658, and Calamy was presented by the trustees of the deceased Robert Rich, 3rd Earl of Warwick, to the rectory of Moreton, where he had preached for some time with acceptance.
Like his father, he welcomed the restoration of the monarchy, and in 1661 he gave generously to the voluntary contribution for the supply of the king's exchequer.
In 1665 he was chaplain to Sir Samuel Barnardiston, at Brightwell Hall, near Ipswich, but returned to his father in the following year, and was with him till his death.
On the king's declaration of indulgence, 15 March 1672, he took out a license and quietly ministered to a small congregation at Curriers' Hall, near Cripplegate.
With his brother Benjamin Calamy, who became incumbent of the parish in which he lived, he was on excellent terms, and among his intimate friends was Richard Kidder, afterwards bishop of Bath and Wells (originally a nonconformist).
He died suddenly in the night, while on a visit in May 1685 to the astronomer Edward Haynes, of Totteridge, near Barnet, a member of his flock.