Under the government of the Cretan Independent State, it was proposed that the Loggia be used as an archaeological museum, but this idea was abandoned in 1904 when the building was judged unsafe. In the same year indiscriminate demolition work began on the first floor.

The following year the Loggia and Armeria (Venetian armoury) were made over to the municipal authority for use as offices. It was not until 1915 that restoration work began, under the supervision of Maximilian Ongaro, curator for artistic monuments in Venice.

After much delay, in late 1934 the Armeria was finally handed over for use by the town council. Reconstruction work on the monument was resumed after World War II, with the aim of linking the Loggia to the Armeria via an atrium.