"[5] St Margaret's was rebuilt from 1486 to 1523, at the instigation of King Henry VII, and the new church, which largely still stands today, was consecrated on 9 April 1523.

In 1878, the church's interior was greatly restored and altered to its current appearance by Sir George Gilbert Scott, although many Tudor features were retained.

[8] In 1863, during preliminary explorations preparing for this restoration, Scott found several doors overlaid with what was believed to be human skin.

The historians believed that William the Sacrist was flayed alive as punishment and his skin was used to make these royal doors, perhaps situated initially at nearby Westminster Palace.

Piper's unified scheme filled each window with an uncompromisingly modern abstract design, intended to create a "total impression of living radiance, in shades of silvery grey predominantly with splashes of pale greens, yellows and blues in varied density, to filter the daylight."

The new windows were dedicated on 15 January 1967 in memory of Canon Carnegie and his wife, Peter Kemp-Welch, Clarence Fletcher and Richard Costain.

[22] On Easter day 1555 in the reign of Mary I a Protestant ex-Benedictine monk, William Flower inflicted wounds to the administerer of the sacrament.

During the First World War, Edward Lyttelton, headmaster of Eton, gave a sermon in the church on the theme of "loving your enemies", promoting the view that any post-war treaty with Germany should be a just one and not vindictive.

In September 2023, a new choir for girls aged 11 to 17 was formed, to sing for regular liturgical services alongside the professional singers of the St Margaret's Consort.

[34] Mackenzie Walcott lists the following as officiating clergymen:[35] Under the Ecclesiastical Commissioners Act 1840, this rectory was annexed to the canonry of Westminster Abbey then held by Henry Hart Milman, such that he and his successors as Canon would be Rector ex officio.