Efforts to secure legal protection for the Venetian monuments began in 1931, when the remains of the old and new fortifications — together with the moat and outer bastions — and the Venetian Loggia were designated as protected monuments. After the destruction of the war, further listings followed in 1947: the arsenals, thirty churches, four houses, two underground cisterns and seven fountains were likewise declared monuments.

These administrative measures did not, however, prevent demolitions — most notably that of the Loggia in 1937. From the early 20th century, the city and its fortifications stood in persistent opposition, to the point that the complete demolition of the walls was proposed in order to release land for development. Ultimately, the fortifications were spared largely because of their sheer scale: their levelling would have entailed prohibitive cost.
A dedicated Ephorate of Antiquities responsible for Crete’s medieval and Venetian monuments was established only belatedly, in the 1960s. In 1965, the Municipality of Heraklion — whose boundaries broadly coincided with the outer defensive zone — was designated an archaeological site. Yet during the years of the military dictatorship (1967–1974), significant monuments were demolished, the most striking example being the Church of the Saviour in 1973.

It was not until 2012, in a renewed effort to safeguard the surviving monuments and archaeological remains, that the boundaries of the city’s archaeological site were clearly defined, encompassing the area within the Venetian walls and moat, together with a surrounding protection zone. Since then, the Ministry of Culture and the Municipality of Heraklion have undertaken systematic joint initiatives for the conservation, restoration and enhancement of the city’s monumental heritage.