John Innes remained a bachelor until his death on 8 August 1904 and was buried in the churchyard of St Mary the Virgin, Merton Park. He left most of the grounds of the Manor House to be converted into a public park for the benefit of the residents of the parishes of Merton and Morden. He left funds and his home, Manor Farm in Watery Lane, and its grounds for the creation of the horticultural institute which still bears his name, the John Innes Centre. His bequest to the nation was to be used for either a school of horticulture that would provide "technical instruction in the principles of the science and art of horticulture and the application thereof to the industry or employment of gardening", or a public museum for the collection of paintings and other works of art. In 1906, the trustees asked the Charity Commissioners to prepare a scheme and by 1908 the scheme was approved by both trustees and Board of Agriculture. On 12 January 1909 the scheme came into force and in 1910 the John Innes Horticultural Institution opened.