Zakros is located on the southeastern tip of Crete, in a natural bay protected from the northwest winds. The archaeological significance of the site was known from 19th century traveler reports. In the early 20th century, the British archaeologist D.G. Hogarth conducted research in the area and brought to light part of a Minoan settlement with remarkable finds. The most important of these was a rich archive, with approximately 300 sealings bearing religious-cult representations and a Linear A tablet.

In 1961 CE, Nikolaos Platon arrived in the area to investigate the origin of important accidental finds, which had been handed over by the residents and, in his opinion, indicated the existence of a palatial center. At the end of the same year, excavations began at three pre-selected sites with the aim of locating it. In fact, the archaeological research, which covered approximately 30 excavation periods, brought to light a palace that had remained intact after its destruction, with impressive findings.

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Initial human presence at ancient Zakros (Kato Zakros), situated on the far eastern coast of Crete, extends chronologically back to the Neolithic period, with continuous sedentary occupation establishing a distinct coastal town by the Early Minoan III to Middle Minoan IA phases (circa 2000 BCE).

The site transitioned into a major administrative and maritime node due to its naturally sheltered, strategic harbor, effectively serving as the primary Minoan gateway for direct trade with Egypt and the Near East. Monumental civic architecture crystallized with the construction of the Old Palace around 1900 BCE, an administrative complex subsequently destroyed by a severe seismic event circa 1700 BCE or during the transition to the Neopalatial period. The New Palace, constructed over the ruins circa 1600 BCE, covered roughly 8,000 square meters, featuring a central court, multi-storied peripheral structures, an internal drainage infrastructure, and specialized workshops.

The absolute cessation of palatial administration occurred rapidly during a widespread destruction horizon circa 1450 BCE, at the end of the Late Minoan IB period, caused by a combined seismic and conflagration event likely associated with the regional disruptions of the Thera eruption.

Because the destruction was sudden and the site was never systematically looted in antiquity, 20th-century CE excavations led by Nikolaos Platon recovered extensive unplundered assemblages in situ, including unbaked Linear A archival tablets, imported Syrian elephant tusks, Levantine Canaanite jars, and Cypriot copper ox-hide ingots. A restricted, highly degraded reoccupation footprint persisted on the surrounding hillsides during the Late Minoan II through Late Minoan III periods, before ancient Zakros was completely abandoned by circa 1200 BCE.

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Minoan Palace
The palace of Zakros that survives today was founded during the Neopalatial period. It is structured around a rectangular central courtyard (inspect), in four wings, like the other known Minoan palaces. The functional areas in the various wings follow the layout of the palace of Knossos: to the west of the courtyard are the sanctuary and the palace storerooms, while to the east are the areas of possible residence and social life. The preparation and consumption of food took place in the northern wing, while the southern one housed the palace workshops. The building, which had at least two floors, was surrounded by a precinct forming internal gardens.

The economic prosperity of the palace center of Zakros during the Neopalatial period is certainly due to the role it played in the maritime "trade" of Minoan Crete with other centers of the Aegean and the eastern Mediterranean. Evidence of its relations with the East is the discovery, in a warehouse in its western wing, of four elephant tusks and six bronze talents (units of cast copper), certainly imported to the site on the same overseas trip.

The settlement developed around the palace, on two hills. About 35 houses were excavated, which, in some cases, were considered palatial annexes. The houses on the north-east hill are separated from the palace by a paved road leading to the harbor and for this reason it was called "Port Street" or the harbour street. The 3 meter wide slab paved guttered road was built during the Proto Palatial period and led to the northeast gate of the palace. Between the buildings, there were stepped paved roads, with pipes for the collection and removal of rainwater (hydraulic management), which delimit large building blocks. The habitation was very dense and for this reason there were no outdoor spaces. The destruction of the city and the palace occurred suddenly around 1450 BCE, simultaneously with the destruction of most residential sites in Crete that mark the end of the Neopalatial period.

Scholarly opinions regarding the causes of these disasters differ: according to one view, they were due to some large-scale natural phenomenon, perhaps a terrifying earthquake, while according to another they were the result of internal conflicts, either between the various Minoan centers or between distinct social classes.

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West Wing
The western wing of the palace complex housed the religious center and the storage magazines of the palace. The storage magazines consisted of two large, semi-subterranean rooms equipped with a window in the western wall, where 23 pithoi were placed against the walls and in two small rooms, while the recesses in the corridor were also used to store pithoi and other vessels. The magazines's small capacity in relation to the other palaces implies that the palace of Zakros relied heavily on sea trade rather than its own agricultural economy.

South of the magazines were the sacral rooms and two large luxurious halls; the "hall of ceremonies" (inspect) and the "banquet hall" (inspect). The two halls were probably paved with wooden floors coated with red plaster with various geometric designs. The hall of the ceremonies contained a square, paved lightwell. In the "banquets hall" two sets of transport and serving vases were discovered.

The sacral rooms consisted of small spaces, a storage room for pottery vessels, the archive (inspect: this chamber yielded clay tablets with Linear A script), the storage rooms for ceremonial vessels and a small shrine with a bench (inspect). Next to the shrine was a lustral basin. The so-called "treasury of the shrine" contained an intact set of ceremonial vessels, including more than fifty stone vases in various shapes imported from different areas.

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South Wing
The south wing is a a relatively square, covering an approx area of roughly 300 square meters. This section lies at the south-western end of the central court . It has been interpreted as a two story workshop, because of the raw materials and semi-worked items discovered here; such as; marble, rock, crystal, faience, and ivory etc. It has also been suggested that this area was also used for the production of perfumes as well.

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East Wing
The east wing was completely destroyed by the cultivation and its walls / structures are scantly preserved above foundations. In the east wing, the excavator identified the king's and queen's quarters (inspect).

The queen's megaron contained a lustral basin (inspect), which was accessed via a set of steps leading down to a subterranean room, which was connected with ritual purification ceremonies. This room, was decorated with frescos depicting Horns of Consecration between pillars placed in cavaties on tall benches. The two main apartments fo the east wing, were connected by polythira-walls, pierced by multiple doors. In the eastern section of the apartments in the center of a great hall, there was a circular cistern (inspect) with a flight of stone steps roofed by a circular lightwell, which was supported by five columns. The hall was accessible through a rectangular portico. The excavator thought that the hall had a similar function to the "throne room" at Knossos.

The "well of the fountain" (inspect) lies south of the circular-cistern hall and is a rectangular structure, supplied by an underground spring, possibly used for watering the gardens. Alongside it is a circular well (inspect) roofed inside a square building. Excavations inside the well recovered clay cups that were used for offerings; one of them was full of olives which preserved their skins.

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North Wing
The north wing of the palace complex consisted of a large hypostyle hall, which was identified as the kitchen area. The identification was based on the large quantities of animal and bird bones, as well as a tripod cooking pot with food remains, that was discovered in the small structures built and used as cooking hearths. The smaller chambers to the east were used for storing cooking pots and other culinary equipments.