The arsenal played a key role in Zamość’s fortification plans from when work began on its defences. Construction of the original timber building took place from May 1582 to July 1583, based on a design by Bernardo Morando.

We can see a building fitting this description called the "armamentarium" on G. Braun’s 1617 plan. Changes in the town’s architecture – the Lubelska Gate being bricked up and the resulting change in transport routes - meant that the arsenal was moved to the other side of town close to Bastion III. The new brick-built building was most probably designed by Andrea Dell'Aqua.
It’s likely that originally the building looked very different to how it does today. The Arsenal burnt down in 1658. This necessitated major renovation work obliterating its original shape. During the fire the arms stored in the arsenal were also lost – going up in flames or melting along with the ruined building.
The building’s overall structure and layout of the rooms was dictated by the arsenal’s functions – its role as an arms and artillery store in a citadel, as well as an armoury housing interesting specimens acquired or seized by the powerful nobleman and magnate, Jan Zamoyski. This use of the store rooms was referred to in the journals of the secretary of the papal legate, Bonifacy Vanozzi. He wrote about a plaque in the arsenal that said: "Pro bombardis tum bello Moscovilico portis, tum ab omnis principibus et civitatibus donatis, tym densique sup juscu, Joannes de Zamoscio, regni Poloniae cancellorius, exercitusque dux supremus F.C. anno orbis redem. MDXXCII." In the 17th century, especially after the fire, the arsenal was just used as an arms store for the town and Estate. The most valuable cannons were not in the fortress, as they had been lent to the Crown’s forces during wars with Sweden. The Arsenal’s time as somewhere to keep Jan Zamoyski’s arms collection was just a brief episode in its long history, often marked by war. Rebuilding in the 19th century changed the building’s proportions, but not its function. When the state took over the fortress from private owners Zamość’s Arsenal became a military facility, initially for the Polish and then Russian armies. Zamość fortress was decommissioned in 1866 - ending its history as an arms store. In the late 19th and 20th century it had a variety of uses: a warehouse, school and factory.
In 1976-1980 the building underwent major renovation as part of the Old Town conservation and restoration project. In October1984 an exhibition entitled “Military traditions in the Zamość region 1580-1984” was opened on the Arsenal’s ground floor.
At the same time an open air exhibition was being organised in the former fortress grounds surrounding bastion III. The exhibition "Artillery and armoured vehicles from World War II" was opened to the public in 1987. The open air display became a key exhibition to look out for on the Zamość region tourist map. The open nature of the exhibition attracted many visitors. The collections of militaria have been displayed at numerous temporary exhibitions at the Arsenal. Thanks to its large, open display space the Arsenal has also been used in major, spectacular, historical and artistic exhibitions, such as “The Zamość Estate library: from Jan to Jan”, opened to the public in 2005, on the 400th anniversary of the death of the town’s founder, Jan Zamoyski.