A previous fortress, the Fuerza Vieja (Old Force), was badly damaged in 1555 during an attack on Havana by the French privateer Jacques de Sores and eventually was demolished in 1582. In 1558 Bartolomé Sánchez, an engineer appointed by Phillip II of Spain, began work on the new fortress, initially known as the Fuerza Nueva (New Force). The Fuerza Vieja was set back from the harbour, but the new fortress was planned to be closer to the harbour to give it a better strategic position. The ironworks were established in 1558, but the first stones were not laid until 1562. Construction was delayed due to complaints from local residents forced to relocate to make way for the building and from disagreements between Sánchez and the Governor of Havana. The fortress was not completed until 1577, with slaves and French prisoners providing most of the labour. Built of limestone quarried from the Havana shoreline, the fortification incorporated thick sloping walls, a moat and drawbridge. The governor, Francisco Carreño, ordered the addition an upper storey as barracks and a munitions store, but on completion, the fortress proved to be too small for practical use.
Despite being positioned closer to the harbour than the Fuerza Vieja, it quickly became apparent that the new fortress was still too distant from the mouth of the harbour to serve effectively as a defensive bulwark, so was instead adopted by Juan de Tejeda as the residence of the Governor of Havana. Subsequent governors made changes to the building, and in 1634, Juan Vitrián de Viamonte added a watchtower with a weathervane sculpted in the form of a woman, by Gerónimo Martín Pinzón, an artist from Havana, and based on the figure crowning La Giralda in Seville. Although the reason for the choice of this figure, called La Giraldilla, is not known, a common suggestion is to honour Inés de Bobadilla, Havana's only female governor, who assumed control from her husband Hernando de Soto when he undertook an expedition to Florida. She spent many years scanning the horizon for signs of his returning ship (unbeknown to her, he had died). The figure became the symbol of the city of Havana (it features on the Havana Club rum label), and is now held at the City Museum housed in the Palacio de los Capitanes Generales in the Plaza de Armas, while a copy is in place on the watchtower. The façade of the fortress was demolished in 1851 to allow O’Reilly Street to go all the way to the docks, and prevent El Templete, completed in 1828, from being overshadowed by the fortress.
The fortress was home to the National Archive from 1899 and the National Library from 1938 up until 1957, when both were relocated to a purpose-built library in Plaza de la Revolución. After the Cuban Revolution in 1959, it housed the offices the National Commission of Monuments and the Centre of Preservation, Restoration and Museology. Used briefly as the Museum of Arms, the conditions within the fortress were not conducive to the preservation of the displays. In 1977, on the 400th anniversary of completion, the building was inaugurated as a museum and used to display exhibitions of Cuban contemporary and international art. In 1990, it became the National Museum of Cuban Ceramics, but as of 2007, no displays are housed in the fortress. Some restoration work was carried out on the fortress prior to the inclusion of the fortification in the UNESCO World Heritage citation for Old Havana.