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The Reformation reached Jersey in severely Calvinistic form in around 1550. As was the case with all the Jersey churches, virtually all traces of the ancient worship were swept aside. The Jersey historian Rev G. R. Balleine gives a graphic account of what happened in St Clement:
Altars, images, stained glass, all were smashed to pieces. Endowments for masses and lamps were confiscated to the Crown. Only one bell was left. Soler, the first Protestant Rector, a fiery Spaniard, who had been a Dominican Friar, did his work so thoroughly that nothing remains today but one empty bracket (on which once stood the statue of a saint), the piscina in the chancel (at which the Priest used to cleanse his hands before Mass), and in the North Chapel a much more primitive piscina together with an ambry (the cupboard which contained the altar vessels, the consecrated oil for anointing the sick, and the reserved sacrament).
During the hundred years following the Reformation, the church became a “Huguenot Temple”, that is to say, it adopted the French Protestant form of worship (except for five years under Queen Mary, when the Catholic ritual was restored, and for a short period during which Dean David Bandinel secured a reluctant use of the Prayer Book). During this time, the men entered by the west door, and the women by a door (now walled up) at the end of the north transept. The south door did not exist at that time. A large gallery was erected at the west end of the church in the days of the Commonwealth (1649-1660) and the stone altar was removed from the east end. Instead, a long oak table was set in front of the pulpit and Holy Communion would have been celebrated four times a year (Christmas, Maundy Thursday, Easter and Whit Sunday) from the north side of this table. It is now situated in the vestry.