The Commissariat Store was constructed of local stone in 1828 to 189 by Moreton Bay penal settlement convicts as a two-storey provisions store near the Brisbane River and what was to become Queen's Wharf. A third storey of rendered brick was added in 1913 to accommodate its continuing use as a government store and providing an address to William Street.

In 1823 Moreton Bay was chosen as a penal settlement for secondary offenders or those who had re-offended while serving their sentence of transportation in Australia. It was intended to better control these convicts and affect a reform in them through isolation, hard labour, strict discipline and harsh living conditions. In 1824 Lieutenant Miller arrived at Redcliffe with 30 convicts. As this location proved unsuitable, the settlement was moved in 1825 inland to a ridge overlooking and bounded on three sides by the Brisbane River, and simple buildings were constructed to serve it.

Penal colonies were run on a military system and so a commissariat directed the procurement, supply and distribution of essential goods, as well as serving as a custom house and bank. The first building used for this purpose in what would become Brisbane Town at Moreton Bay was a slab structure in the vicinity of the current intersection of Albert and Elizabeth streets. There were two other store structures at Amity Point and Dunwich on Stradbroke Island. In 1826 Captain Logan arrived as Commandant and began a works program that replaced key buildings with more substantial structures made of stone and brick. One of these was the Commissariat Store. Along with houses for the Commandant, Commissariat officer and chaplain, it was erected on the ridge running parallel to William and George Street that remains the focus of government to the present day.

A position near the river bank was selected for the new store, following recommended procedure, to allow goods to be conveniently loaded and unloaded from a wharf. This also provided a single point for the entry and distribution of tools, weapons, clothing and food rations to permit secure control of such vital supplies. The design was by William John Dumaresq (1793-1868) whose plans arrived from Sydney in April 1828; work on the foundations commencing some months later. Dumaresq was also responsible for the design of the store at Dunwich completed in 1828.

The original river bank in this area was quite steep and the underlying rock was quarried to create a relatively level building platform. The excavation work was heavy and carried out by the Gaol Gang of convicts as a specific punishment, but the masonry and other construction work required skilled labour and was most likely supervised by Lieutenant Thomas Bainbrigge, sent especially from Sydney with suitable workmen in 1827 and made Superintendent of Works for the colony the following year. Some time after retaining walls were constructed around three sides of the store building; the one to William Street appearing in an 1838 cross-section and the two at each side in Petrie's front elevation of the building also dated to that year.

In common with the settlement's other new buildings, the Commissariat Store followed a simple design suitable for everyday use in a penal colony and was well constructed from local materials.

The first outpost of the convict colony in Australia had been established in New South Wales in 1788, the settlement being almost immediately extended to Norfolk Island (abandoned in 1814 and re-established 1825), and then to Tasmania, to Newcastle (later to Port Macquarie), Moreton Bay and then to Western Australia. The only convict-built Commissariat Stores that survive today, aside from that in Brisbane, number seven. Two remain in WA in Fremantle (1852) and Guildford (1853 to 1854). Four remain in Tasmania and are listed in its state register.