In the early 20ies, interventions occurred on the upper terrace of the fortress, aiming to rearrange the auxiliary buildings into rooms for the accommodation of the lighthouse keeper and the Sea Scouts. Around 1920 the “Committee for the Harbor of Heraklion” installed on the upper terrace power poles and a crane, which collapsed during the W.W. II bombardments. At that period, the NE side of the Fortress had been undercut by the sea-weaves. The problem was solved when the extension of the NW breakwater was constructed.

The first restoration campaign took place in 1959 under the supervision of the archaeologist Stylianos Alexiou and included the demolition of the half-ruined Ottoman battlements along with some modern constructions, the removal of the embankment of the terrace, especially on the southern and eastern side, and the restoration of some canon-openings. The demolition of the modern constructions of the western and northern side of the terrace took place in 1969 under the supervision of the archeologist Emmanuel Borboudakis, who also conducted a more systematic restoration campaign between the years 1972-1975, according to an official plan executed by the architect A. Lambakis. During the campaign, the entire corridor of the battlements and the cannon-openings of the upper terrace were restored, the terrace itself received a stone-pavement, skylight-windows on stone-parapets were added, a facility-building was constructed at the northern edge of the terrace, another building at the western edge was rearranged to act as scenery background for the small open-air theater that was installed and the facades of the southern buildings were reconstructed. The vaulted chambers on the ground level were cleaned up of embankments and their floors were covered with stone pavement; wooden doors and shutters for the canon-openings were added as well as electricity, water and drainage installations. The southern facade of the fortress was also restored and the access to the Venetian and modern breakwater was improved.

In 2002 the 13^th Ephorate of Byzantine Antiquities restored parts of the battlements’ parapet. In 2007 the undercuts (or perhaps underwater canals) were restored by “Heraklion Port Authority S.A.” according to a plan executed by the “Eastern Crete Development Organization”.