The building that today houses the Archive was built to accommodate the ever increasing number of traders who congregated around the Mercaderes University (converted into consulate in 1546) and required a building of their own to conduct their business and to resolve disputes. The conflict between the cathedral authorities and the merchants over the occupation of consecrated cathedral space for such non-pious activities as those carried out by the traders gave the final boost for the commencement, in 1583, of the construction of the Lonja de Mercaderes building.
The royal architect, Juan de Herrera, was responsible for the design of a building that took until 1646 to complete. The work was undertaken by various prestigious architects, such as Juan de Minjares, Alonso de Vandelvira and Miguel de Zumárraga who, particularly the latter, altered some of the ideas from the original project design by introducing innovative structural elements in the building, such as the vaulting of the upper floor, to lighten Herrera's traditional solution of a double sloped roof, which would have been heavier and a greater fire risk.
The second half of the 17th century saw the political and commercial decline of the Spanish empire, this inevitably contrasting with the recently completed work on the Lonja building. In 1717 the headquarters of overseas trade was transferred to Cadiz, leaving only a Trade Office in Seville. The building was so underused that it began to be used for private homes, whilst the institution that had instigated its construction fell into decline.
The choice, in 1781, of the Lonja de Mercaderes in Seville as the headquarters for the major project of what was to be the General Archive of the Indias prevented the further deterioration of the building. Once the private residents had been removed from the building and the space allotted for the Trade Office and for the Archive and its related services, Luca Cintora, architect responsible for the Reales Alcázares building, undertook an audacious adaptation of the building for its use as a document depository. His controversial actions resulted, on one hand, in the recovery, as far as possible, of the original building as conceived by Juan de Herrera, reinstating the openness in the galleries, and on the other, in the renovation of the stairway, which was richly faced in marble to give it its current sumptuousness.
The building has a square layout, each side measuring 56 metres, with two levels built around a courtyard surrounded by columns with chains; the Archive building basically consists of a central courtyard surrounded by two square sections, one internal and one external. The whole building is built of stone, with two vaulted floors connected by the monumental stairway.
Recently, the Ministry of Culture has undertaken remodelling work on the building in order to modernise its facilities, improve document storage and make the external galleries of the upper floor suitable for temporary exhibitions, providing an itinerary through the entire building for visitors.
The area for research and management of the General Archive of the Indias, though currently outside this area, is just to one side of it. The building known as the "Cilla" has been remodelled to ensure the compatibility of its administrative functions with research and with visits and exhibitions. This building is supported by the stretch of wall running from the Alcazar towards the Torre del Oro. The building is rectangular, the ground floor supported by pillars and the first floor on columns with Spanish late-Gothic vaulted ceilings. The building also has two added levels, one under the roof, and a basement. This building has been used for various functions since it was taken over by the guild; from 1972 it was used by Seville's City Council to house the city's Museum of Contemporary Art, and it is currently the headquarters of the General Archive of the Indias.