The origin of the structure dates to 1572 when Philip II commissioned the building in from Juan de Herrera, the architect of the Escorial to house the Consulado de mercaderes of Seville. The merchants of Seville had been in the habit of retreating to the cool recesses of the cathedral to transact business.
The building encloses a large central patio with ranges of two storeys, the windows set in slightly sunken panels between flat pilasters. Plain square tablets float in the space above each window. The building is surmounted by a balustrade, with rusticated obelisks standing at the corners. There is no sculptural decoration, only the discreetly contrasting tonalities of stone and stucco, and the light shadows cast by the slight relief of the pilasters against their piers, by the cornices, and by the cornice strips that cap each window.
The building was begun in 1584 by Juan de Mijares, working to Herrera's plans, and was ready for use in 1598, according to an inscription on the north façade. Work on completing the structure proceeded through the 17th century, directed until 1629 by the archbishop Juan de Zumárraga and finished by Pedro Sanchez Falconete.
In 1785, by decree of Charles III the archives of the Council of the Indies were to be housed here, in order to bring together under a single roof all the documentation regarding the overseas empire, which until that time had been dispersed among various archives, as Simancas, Cádiz and Seville. Responsibility for the project was delegated to José de Gálvez y Gallardo, Secretary for the Indies, who depended on the historian Juan Bautista Muñoz for the plan's execution. Two basic motivation underlay the project; in addition to the lack of space in the Archivo General de Simancas the central archive of the Spanish Crown, was the expectation, in the spirit of the Enlightenment, that Spanish historians would take up the history of Spain's colonial empire. It was decided that documents evolved after 1760 would for the time being, remain with their primary institutions.
The first of the documents arrived in October 1785. Some restructuring of the Casa Lonja to accommodate the materials was required, and a grand marble staircase was added, to designs of Lucas Cintara in 1787.
The archives are rich with autograph material from the first of the Conquistadors to the end of the 19th century. Here are Miguel de Cervantes' request for an official post, the Bull of Demarcation Inter caetera of Pope Alexander VI that divided the world between Spain and Portugal, the journal of Christopher Columbus, maps and plans of the colonial American cities, in addition to the ordinary archives that reveal the month-to-month workings of the whole vast colonial machinery, which have been mined by every Spanish historian in the last two centuries.
Today the Archivo General de Indias houses some nine kilometers of shelving, in 43,000 volumes and some 80 million pages, which were produced by the colonial administration:
The structure underwent a thorough restoration in 2002–2004, without interrupting its function as a research library. As of 2005, its 15 million pages are in the process of being digitized.