The first church lost to the Great Fire was St. Margaret New Fish Street; it was not rebuilt, the parish being united with St. Magnus and the site given to The Monument, which stands there yet, 202 feet tall and 202 feet to the east of the spot where the fire began.
The church is first mentioned in the last decade of the 12th century and must have been well known to the many pilgrims and others who crossed over the nearby London Bridge. A fish market was set up in the street in the same century while a City Ordinance of the 14th century required lampreys from France to he sold 'from under the walls of the church'. A further Ordinance of 1379 mentions the conduit, 'hard by the church', as one of the two places where fresh fish could be sold. In the Guildhall Library can be seen the Book of St. Margaret, New Fish Street in which are listed an extraordinary collection of saintly relics. Among the relics claimed were portions of the crib of Christ at Bethlehem, Moses's rod with which he divided the Red Sea, and the 'usual' pieces of clothing for early saints of the church.
During the Middle Ages the parish had two rectors of note. In 1461 John Alcock was appointed rector. He stayed until 1471 when he was made Bishop of Rochester, to be followed by Worcester, and in 1486 he succeeded John Morton at Ely when he became the Archbishop of Canterbury. Alcock was twice Chancellor of England, Master of the Rolls, President of Wales and the founder of Jesus College Cambridge. The other was Geoffrey Wren 1512-1527 when during his stay at St. Margaret's he became a Canon of Windsor. He lies buried under the sixth arch of the North aisle of the Royal Chapel of St. George at Windsor.
John Stow in his 'survay' describes the church as being 'a proper church, but monuments hath it none'. From that we assume that he meant it was a building of some size in good repair. In a survey, 'Valor Ecclesiasticus' during the reign of Henry VIII the rectory was valued at £31 11s. 8d. In 1636 the annual income was shown as £150 which is, presumably, the stipend of Thomas Brooks, a Puritan preacher here during the commonwealth. He was ejected at the time of the Restoration of the Monarch in 1660 when Robert Porey, the legal tenant of the rectory became a prebendary and canon residentary of St. Paul's. At which time George Smalwood became rector of St. Margaret's. The church was the first to perish in the Great Fire of 1666 and was not rebuilt. The monument stands on the site today and a City plaque commemorates the church on a nearby office building.