John Thomas Brooks died at Flitwick Manor on 22 December 1858, a week after his 63rd birthday. Tom Chapman certified the cause of death as extensive ulceration of the lungs, and John Marshall registered the death.

In his Will which John Green of Woburn had drawn up for him on the 8 December, he appointed John Green and Samuel Swaffield as Executors and left his real property to Mary for her life, and thereafter to Johnnie for his life, and thereafter to Sophie for her life (unless she should remarry), and thereafter to their children in entail, extending in default of any heirs to George and Willie and their children. His money was to provide an income for Mary for her life and thereafter to provide legacies: to George £5000 to Willie £5000

The Will was witnessed by John Green and Wynter.

A Codicil of the same date left legacies to the servants:

This Codicil was witnessed by Tom Chapman and John Green

J. T. Brooks was buried in the vault of his forebears, beside Mary Ann, at Maulden, with the text: “Thou shalt keep him in perfect peace whose mind is stayed on Thee. Remember that he trusted in Thee”.

Mary erected an East Window (executed by O’Connor) in the newly restored church at Flitwick to his memory, the theme of which was the Resurrection. Unfortunately in fitting the window in it was found that “from the middle light the stone tracery had long fallen away and when the present window was put in it was thought that the subject could be fitted in more effectively without restoring it” (Petley p.45). More recently the missing tracery was found to be a source of weakness and so the window was removed, the tracery restored, but the O’Connor glass was not replaced as it no longer fitted. However, the window in memory of Mary Ann still survives. Mary died 5 November 1879 at Flitwick and was also buried at Maulden with the text: “the Lord shall be thine everlasting light” (Isaiah 51. 26).

Johnnie retired from India in 1863 and came home to be squire of Flitwick. Like his father he became High Sheriff of Bedfordshire (in 1880). His younger daughter, Marianne, married at the age of 29 the son of an Indian Army friend of her father’s and died in childbirth the following year.