The first human inhabitants of Knossos probably came there from Anatolia in the 7th millennium bce and established an agricultural society based on wheat and livestock raising. At the beginning of the Early Minoan period (3000–2000 bce) they began using bronze and making glazed pottery, engraved seals, and gold jewelry. A hieroglyphic script was invented, and trade with the Egyptians was undertaken. The first palace at Knossos was built at the beginning of the Middle Minoan period (2000–1580 bce). It consisted of isolated structures built around a rectangular court. Knossos produced fine polychrome pottery on a black glazed ground during this period. About 1720 bce a destructive earthquake leveled most of Knossos. The palace was rebuilt, this time with extensive colonnades and flights of stairs connecting the different buildings on the hilly site. The remains of this palace occupy the excavated site in the present day. The administrative and ceremonial quarters of the palace were on the west side of the central court, and the throne room in this area still contains the gypsum chair in which sat the kings of Knossos. This area of the palace also had long narrow basement rooms that served as storage magazines for wheat, oil, and treasure. Workshops were located on the northeast side of the central court, while residences were situated in the southeastern section. An elaborate system of drains, conduits, and pipes provided water and sanitation for the palace, and the whole urban complex was connected to other Cretan towns and ports by paved roads. The art of Minoan fresco painting reached its zenith at this time, with scenes of dancing, sports, and dolphins done in a naturalistic style. The Minoans also replaced their hieroglyphic script with a linear script known as Linear A.

About 1580 bce Minoan culture and influence began to be extended to mainland Greece, where it was further developed and emerged as the culture known as Mycenaean. The Mycenaeans, in turn, achieved control over Knossos sometime in the 15th century bce; the Linear A script was replaced by another script, Linear B, which is identical to that used at Mycenae and is most generally deemed the prototype of Greek. Detailed administrative records in Linear B found at Knossos indicate that at this time the city’s Mycenaean rulers controlled much of central and western Crete.

Some time after about 1400 bce, what Evans called the “Last Palace” of Knossos was destroyed by a fire of uncertain origin, and fires destroyed many other Cretan settlements at this time. Knossos was reduced henceforth to the status of a mere town, and the political focus of the Aegean world shifted to Mycenae on the Greek mainland. Knossos continued to be inhabited through the subsequent centuries, though on a much-reduced scale.