Minoan religion centred around the cult of the goddess of fertility, whose consort dies and is reborn every year, representing the regeneration of nature. The observation of the cycle of nature led to the personification of one aspect of fertility, the young god who dies and is reborn each year. The goddess, the Great Mother, is the spouse of the god. The sacred marriage (a theme which also occurs in the art of later periods) represents the union of the two gods. Ritual ceremonies were performed to secure fertilization and fruitfulness. Similar pairs of gods occur in eastern religions. The birth and death of the god coincides to annual rebirth and the withering of vegetation. Some religious ceremonies resemble magic rites carried out to stimulate the productive function of personified natural forces. Minoan ceremonies related to vegetation suggest the cult of the Mother and the Daughter in the Eleusian Mysteries of the Classical period, which probably dates back to Pre-Hellenic years. Certain archaeological finds from the Late Bronze Age, such as a complex of ivory figurines of two goddesses with an infant from Mycenae lend weight to this view.

Apart from the depictions of the deity and worshippers, sometimes various animals or fabulous creatures of an intermediate human and animal form appear in the cult scenes. They are interpreted as the demons of vegetation, which participate in the cult. However, these figures may not necessarily represent zoomorph deities, but could be priests wearing zoomorph masks during the ceremonies.

The Minoan deity appears in many scenes, which raises doubt concerning the actual number of the goddesses; that is whether there was one or several. The goddess is depicted as the Mother of the Mountains on a mountain peak flanked by two lions; as the Hunting Goddess (Potnia Theron); as the Goddess of the Sacred Tree; as the Snake Goddess; the Dove Goddess or the Poppy Goddess. She also occurs in war representations, with a sword and a shield and sometimes on sea voyages. Another common iconographic theme is the Mother-Goddess nursing an infant. The various symbols of the goddess represent her different aspects. Thus, the snakes represent her chthonic character; the doves are the symbol of the heavens, and the sopoforic poppies are the symbols of the Mother-Goddess calming the infants. One interpretation suggests that these aspects of Minoan religion were conducive to monotheism.

The first fully-rounded elements of Minoan religion appear as early as the Prepalatial period. After the decline of Minoan civilization, Minoan religion influenced the Mycenaean religion and later that of Antiquity. Signs of it appear in some pre-Hellenic names of vegetation deities such as Diktynna, Britomartis, Ariadne and Hyakynthos. Many of the symbols of the Minoan goddess accompany ancient female divinities. Athene, the goddess of war is depicted with weapons, Eileithyia is the goddess of childbirth, Artemis is the goddess of wild animals, Aphrodite is represented with doves, Demeter with the poppies, and lions feature in the cult of Cybele. In the religion of Asia Minor, there are divinities that correspond to the Minoan goddess, such as the Hittite goddess of war which was represented by the panther, the lion and the dove.

In contrast to the female deities, the male gods of the later Greek Pantheon do not correspond to the symbolism of the Minoan world. This shows that the pantheon of Greek Antiquity was probably constituted of male gods of Indo-European origin, in combination with the pre-Hellenic female deities.