Part of the second Church Missionary Society station in New Zealand, the store was designed by John Hobbs to replace an earlier wooden storehouse.

The Stone Store was intended to be the base of the Church Missionary Society's trading post, selling produce from the farms at the te Waimate mission to ships, and European goods to Māori.

Marsden planned to build a flour mill on the adjacent Kerikeri River, but this was eventually built at te Waimate instead.

Following the sacking of Russell (then still commonly known as Kororāreka) in the Flagstaff War, it was briefly taken over by Governor George Grey for use as a magazine and barracks.

After the cessation of hostilities in 1845, the stone store was leased to become the centre of Kauri gum trading operation, and then in 1863 it was used to house a boys' school.