The site was discovered in 1878 by Minos Kalokairinos. Excavations at Knossos began in 1900 by the English archaeologist Sir Arthur Evans and his team, continuing for 35 years. The initial excavations and partial restoration of the palace were conducted under the direction of Arthur Evans in the early years of the 20th century. The size of the palace greatly exceeded his initial expectations, as did the discovery of two ancient scripts, which he named Linear A and Linear B, to distinguish their writing from the pictographs that were also present. From the excavation of the palace, Evans developed a new archaeological concept of the civilization he used, which he named Minoan, following the long-standing practice of labeling all artifacts from the site as Minoan.

The Palace of Knossos was undoubtedly the ritual and political center of Minoan civilization and culture. It presents itself as a labyrinth of workshops, living spaces, and storage areas surrounding a central square. An approximate picturesque view of certain aspects of Cretan life in the Bronze Age is provided by the restorations of the palace's interior and exterior frescoes, as well as by the decorative patterns of pottery and the symbols on the seals.

The palace was abandoned at some unknown time at the end of the Late Bronze Age, around 1380–1100 BC. The exact reason is not known for certain, but one of the many destructions that befell the palace is generally cited. The population that abandoned the area was likely Mycenaean Greeks, who had previously occupied the city-state and used Linear B as their administrative script, in contrast to Linear A, the earlier administrative script. The hill was never again settled or urbanized, although the occupiers may have used it for some time.