The windows in the north aisle were filled with coloured glass in the last quarter of the nineteenth century.

The window at the west end commemorates the poet John Milton (1608-74) who married his second wife at St Margaret's in 1656. In the centre of the window Milton is seen dictating Paradise Lost to his daughters; he is also shown as a schoolboy, and meeting Galileo at Florence in 1638. Other scenes in the window are taken from Paradise Lost and Paradise Regained. The window was the gift of George W. Childs of Philadelphia in 1888.

The monuments below the window include one to Captain Sir Peter Parker (1785-1814), commander of the frigate Menelaus, who died in action on the shores of the Chesapeake river. His body was brought back to St Margaret's for burial and this monument erected by his officers and crew. He was a cousin of the poet Lord Byron, and as a young lieutenant served briefly on Nelson's flagship Victory.

An oval memorial commemorates the Bohemian artist Wenceslaus Hollar (1607-77). He produced important engravings of London, including some of the earliest surviving depictions of Westminster Abbey. He is buried in the churchyard.

The oldest intact monument in St Margaret's is in this aisle. It commemorates Cornelius Van Dun (d. 1577), a native of Breda in the Netherlands, who served as a Yeoman of the Guard under four Tudor monarchs. The portrait bust shows Van Dun in his uniform and the inscription refers to the almshouses he built for twenty poor widows of the parish.

The two eastern-most windows in this aisle survive intact. The first, erected by public subscription in 1880, commemorates Admiral Robert Blake (1599-1657), one of England's great sailors, who fought for the Parliamentary side in the English Civil War. Blake was originally buried in Westminster Abbey, but soon after the Restoration he was reburied, with other Parliamentarians, in St Margaret's churchyard. The lower panels of the window depict Blake on board ship at Malaga; his body being brought by river for burial at Westminster Abbey; and his subsequent re-burial.

The final window commemorates Edward Ashurst Morris (d. 1890). The central Nativity scene is based on a painting by Boticelli in the National Gallery. Above it are dancing angels, and below are allegorical figures of Charity, Brotherly Love and Fortitude.

Since 1981 the east end of the aisle has formed the Chapel of Christ the Intercessor. The furnishings were the gift of Mr and Mrs John Elliott of New York City, who married at St Margaret's in 1956, to commemorate their silver wedding.

The organ

On the north side of the chancel is the organ, although the console is on the south side. The first mention of an organ in St Margaret's is in the church wardens' accounts for 1474. The present instrument was installed by J. W. Walker in 1897 and restored by them in 1978 and 1993.

There is also a small five-stop chamber organ built by Henry C. Lincoln in 1807.

The World Wars

When the First World War ended in 1918 Prime Minister David Lloyd George led the members of the House of Commons to St Margaret’s for a service of thanksgiving. In 1945 Prime Minister Winston Churchill did the same when the Second World War ended.

War damage

St Margaret’s suffered some damage from the intensive bombing of the Second World War. Evidence of this remains today, such as the blackened memorial to The Reverend James Palmer (caused by an oil bomb) and fire damage to some of the pews, such as pew number 38.

The stained glass in the second window in the north aisle was destroyed during the Second World War and the space is filled with plain glass. A similar fate befell the next window, although some fragments of stained glass remain, including one in which William Caxton (the first English printer) demonstrates his printing press to King Edward IV and Queen Elizabeth Woodville. These fragments were moved from the Caxton window’s original place over the East Door, where the Fitzroy window is now.