The church survived the Great Fire of London with only minor damage[1] but subsequently fell into disrepair and was rebuilt in 1788–91.

By the end of the 11th century, Botolph was regarded as the patron saint of boundaries and, by extension, trade, and travel.

The living was originally in the possession of St. Martin's-le-Grand, but on the dissolution of the priory, King Henry VIII granted it to the bishop of the newly founded Diocese of Westminster.

A Cluniac foundation, it was suppressed by King Henry V as an alien house, and its lands and goods were granted to the parish of St Botolph.

[13] The new church was built of brick, with a low square bell tower at the west end constructed on the remains of its stone predecessor.

[13] The plain exterior is in contrast to what John Betjeman called an "exalting" succession of features inside.

[14] The interior has wooden galleries supported on square panelled columns, a semi-circular apse with a half dome, a highly decorated plasterwork ceiling, and, at the east end the only 18th century stained glass window in the City of London, a depiction of The Agony in the Garden[15] painted by James Pearson.

[16] The east façade, towards Aldersgate Street, is a screen wall, erected in 1831 and executed in Roman cement, with a pediment and four attached Ionic columns standing on a high plinth, with a Venetian window between them.

[16] In March 2023, after the Church of England's General Synod approved the principle of blessings for same-sex couples, the guild vicar of St Botolph's was announced as "acting area dean" of a new "deanery chapter", separate from the official diocesan structures, for clergy who felt "compelled to resist all episcopal leadership from the House of Bishops".