In 1604, the Order's arsenal was transferred to the Grandmaster's Palace by Alof de Wignacourt, and was housed in a large hall at the rear of the building.

[2] In the late 1850s, the armoury was restored under the personal direction of Governor John Gaspard Le Marchant, and it opened to the public as a museum in 1860.

[2] In World War II, the hall housing the armoury was damaged by aerial bombardment on 7 April 1942.

[2] In 1969, UNESCO sent Polish experts Aleksander Czerwiński and Zdzisław Żygulski to make an inventory of the armoury, and they called it one of "the most valuable historic monuments of European culture" in their report.

[2] In 1975, the collection was transferred from its original location to two former stables on the palace's ground floor, where it remains today.