During the Commonwealth, All-Hallows-the-Great was a centre for the Fifth Monarchy Men, a millenarian sect that preached the coming of the reign of saints following the demise of the fifth rule of kings, as prophesied in the Book of Daniel.

[4] The effect of the radical doctrine on the congregation may be surmised by Samuel Pepys's account of their setting up the Royal coat of arms of Charles II, one month before the Restoration.

After the Restoration, however, the parish petitioned the Archbishop for the retention of Robert Bragge, the Commonwealth incumbent, who they claimed was "sound in doctrine and of a holy conversation."

A new tower was built on the south, but in 1894, the rest of the church was demolished, the furnishings dispersed and the parish combined with that of St. Michael Paternoster Royal.

This, in turn, was demolished in 2006, to make way for low-level office development now known as Watermark Place The church was a slightly irregular rectangle with exposed north and west frontages.

The request sent by the Church Commissioners to Wren that "the Tower of All Hallows-the-Great be forthwith finished with a cupola or spire as you shall best approve of, by reason it stands conspicuous to the Thames" was never acted upon.

It was one of two Wren churches to have a rood screen, commissioned by the parish after seeing that erected for St Peter upon Cornhill (the tradition that it was a gift from a member of the German merchant community is without foundation).

[clarification needed] The life size images of Moses and Aaron flanking the Decalogue on the reredos are now in St Michael Paternoster Royal, which also received the lectern (now stolen) and the chandelier.