In the 13th century, as Turku emerged as the most important trading center in Finland, the bishop's seat moved from its previous location at Koroinen further up the Aura River to a mound called Unikankare in the middle of the growing town. Bishop Magnus I consecrated the new stone cathedral on June 17, 1300, dedicating it to the Blessed Virgin Mary and Saint Henry, traditionally considered the first Bishop of Finland. The original building was smaller than what stands today, with a lower roof and its east front roughly where the pulpit now stands. But the foundation was laid, both physical and spiritual. For the next seven centuries, this would be the center of Finnish religious life, first Catholic, then Lutheran after the Reformation swept through in the 16th century.

Throughout the Middle Ages, the cathedral grew and changed. A new choir with octagonal Gothic pillars was added in the 14th century. Side chapels multiplied along the nave until there were 42 in total, each with altars dedicated to various saints. The reliquary tomb of Bishop Hemming of Turku survives from this period. Hemming, who died in 1366, was a close friend of Saint Birgitta of Sweden and a significant benefactor of the cathedral. Pope Leo X recognized him as blessed in 1514, and his remains were moved to a specially prepared niche. The wooden reliquary chest, though its original bright colors of gold, yellow, blue, and red have dulled over time, still holds the bones of this medieval holy man beside the pulpit.

Among the notable people buried within the cathedral is Karin Mansdotter, one of the most remarkable figures in Swedish royal history. A peasant's daughter who became Queen of Sweden as the wife of Erik XIV, she lived many decades of her life in Finland after her husband was deposed. When she died in 1612, she was buried under the floor of the Tott Chapel. In the 1860s, a memorial committee raised her remains and moved them to the Kankas Chapel, where she now rests in a black marble sarcophagus decorated with a crown on a golden pillow. Other notables share the cathedral floor: Princess Sigrid of Sweden, Scottish mercenary leader Samuel Cockburn, and Torsten Stalhandske, an officer in the Thirty Years' War.

The Great Fire of Turku in 1827 destroyed most of the city and devastated the cathedral. The interior of both the tower and nave burned, and the old tower roof collapsed. What rose from the ashes was partly new creation. The present spire, reaching 101 meters above sea level, was constructed after the fire and has become the symbol of both cathedral and city. Swedish artist Fredrik Westin painted the altarpiece depicting the Transfiguration of Jesus in 1836. German architect Carl Ludvig Engel, famous throughout Finland, designed the reredos and pulpit. Court painter Robert Wilhelm Ekman covered the chancel walls with Romantic-style frescoes depicting the life of Jesus and two pivotal moments in Finnish church history: Bishop Henry baptizing the first Finnish Christians and reformer Michael Agricola presenting King Gustav Vasa with the first Finnish New Testament.

The cathedral remains central to Finnish national life. Its bells at noon are a daily reminder of continuity stretching back seven centuries. Each Christmas Eve, the Declaration of Christmas Peace is proclaimed from the Old Great Square beside the cathedral, a tradition since the 13th century. The current main organ, built in 1980, features 81 ranks with mechanical action. An extensive renovation scheduled from February 2026 to late 2028 will modernize the building's systems while preserving its historic character, timed to conclude before the 800th anniversary of Turku. The cathedral will be closed during this period, but when it reopens, the bells will ring again at noon as they have for centuries, broadcasting across Finland the steady heartbeat of the nation's oldest continuous religious tradition.