Between 1886 and 1915 the area inside the castle walls was the subject of no less than seven excavation campaigns, directed first by Alessandro Prosdocimi and then by Alfonso Alfonsi. The purpose of these excavations was to prove the actual existence of the remains of the castrum and the ancient residence of the Este family, feudal lords of Este, which had grown up from the 10th century and was destroyed in the 13th century. The finds were left in view and equipped for visiting, but were later partly reburied and abandoned to decay until they ended up, in very recent times, completely forgotten under the garbage in the municipal public garden or under piles of road construction material.
A resumption of research took place from 1990 until 1996 with Edi Pezzetta and Angela Ruta Serafini and with the start of the expansion of the Archaeological Museum, housed in the surviving wing of Palazzo Mocenigo.
There are currently two medieval archaeological areas in the Castle area equipped for visiting: one in the basement of the museum (by permission) and one at the top of the hill where the core of the first Este castle was located.