João Francisco, a Portuguese whale fisherman, established a small whaling port at the north of Itaparica Island in 1624. The point was called Ponta da Baleia. The point was occupied by the Dutch during their occupation of Brazil. The Dutch, under Siegsmundt Van Schkoppe, established a small earthwork fortification in 1647 at the Ponta da Baleia. The structure sat on a hill protecting the only natural port on the island. The Dutch named the fortification the Fort of the Eminence. It resisted an attack by Francisco Rebelo in October 1647. The Dutch destroyed the fortification when they retreated to Recife. , governor of Bahia, planned a reconstruction of the fort in 1704. Miguel Pereira da Costa, a military officer from Portugal, arrived in Brazil in 1710 and identified the northern point of Itaparica as a strategic location to protect the Bay of All Saints; the point protected both the Bay in general, and small boats from the Recôncavo region in the interior of Bahia that supplied Salvador with much of its trade. Pereira da Costa appealed to Lourenço de Almeida, governor, for funds to complete the fortification. The French invasion of Rio de Janeiro in 1711 spurred the Portuguese to fund the project on the site of the Dutch fortification. Sancho de Faro, governor of Brazil, inspected the fort and its military works in 1719. It was again inspected in 1722 and described in subsequent reports, and again repaired in 1782. The Forte de São Lourenço played an important role in the Brazilian struggle for independence. Barros Galvão, a Brazilian independence fighter, scaled the walls of the fort, now abandoned by the Portuguese, to search for any remaining weapons and to occupy the fort. Brazilian forces repelled attacks by the Portuguese on January 7, 1823. The fort subsequently became the property of the Brazilian Navy. The fort was in ruin by 1859, as recorded during a visit by Dom Pedro II. Its cannons were useless by this point and the Command House was used as a public jail. The fort was rebuilt between 1862 and 1863 as part of the repair of forts across Brazil. It was transformed into a hospital in 1892.
The fort consists of walls of stone masonry with access via a tunnel and a ramp. It covers. The fort consists of two "irregular hornwork demi-bastions" of six protruding angles and two reentrant angles. The structure was built to defer both attacks by sea and from infantry attacks by land. The fort had a captain's residence, barracks, and prison. The former barracks and prison are covered by cradle vaults. The internal structures were modified or removed in 1970 by the Brazilian Navy. The fort was remodeled into a degaussing station by the Brazilian Navy between 1974 and 1975; the Command Houses was demolished and a U-shaped structure of reinforced concrete housed a degaussing station.