In 1598, Engineer-in-Chief Tiburcio Spanocchi proposed building a small castle to guard the entrance to the port of Pasaia, but it was not until 1620 that Julio Oviedo and Captain Francisco Lupecio drew up the first fortification project, with a castle close to an old mill (Txurrutella-errota). The fortification was not completed due to lack of finance, and only the gun platform was built during this first phase.
The work was further slowed down in 1633 as a result of disagreements between the engineers Jerónimo de Soto and Pedro Palear "Fratín". In 1638 and 1719 the unfinished castle was taken by French troops, who made important alterations. Later work gave the fortress the appearance it was to retain until the early twentieth century.
On the seaward-looking side there was a thick uneven wall in six sections of different lengths, facing in different directions, which served to contain the terreplein (sloped embankment) of the main platform. Four gun emplacements were built on the side of the parapet directly overlooking the mouth of the harbour canal with another three below them in underground casemates. A sentry box was erected at the intersection between two walls.
The landward side consisted of a high wall, atop which troops were protected by a low parapet. The wall was formed by nine short curtains facing in different directions, with a small building (first used to house the chaplain and later as a barracks for the artillerymen). A larger four-storey building sheltered behind the same wall, at a lower height. It had a rectangular plan and served as a barracks.
St. Elizabeth's Castle was decommissioned in 1867, although it was occasionally used in later years. The gun platform, the main feature of the castle, was destroyed in the first half of the twentieth century during work to improve the port's entrance canal. It is now a private residence.