The Royal Villa was built in the 16th century B.C. (New Palace period). After the destruction of the palaces in 1450 B.C., only a small "megaron" of the "Mycenaean" type was built in their place. There is evidence that in the Geometric period (8th century B.C.) the site had religious function.

In the Hellenistic period (4th-3rd centuries B.C.) the sanctuary of Zeus Velchanos was founded and much later, during the Venetian occupation, the area of the courtyard was occupied by the church of St. George Galatas (14th century A.D.).

The Italian Archaeological School at Athens located and excavated the site of Aghia Triada in the years 1902, 1903, 1904-1905 and 1910-1914.

The Villa at Aghia Triada consists of two wings which form an L-shaped structure enclosing a court. Although it does not have the dimensions of the palaces at Knossos and Phaistos, it presents all the typical features of Minoan palatial architecture. It has halls with polythyra (pier-and-door partitions), light-wells, shrines, storerooms, repositories, workshops, staircases, porticoes, courtyards, terraces and balconies, streets and courtyards paved with flagstones. Numerous finds were uncovered in the villa during the excavations.