Historians do not unanimously agree on the founder of the church. One possibility is Duke Henry II the Pious (1196–1241), the son of Prince Henry the Bearded (1165–1238), who resided in Kraków and previously invited the Franciscans to Wrocław. His wife, Anna (daughter of the Bohemian King Premysl Otakar I), and especially her sister Agnes (Agnieszka), also played a significant role. Another figure widely regarded as the founder is Duke Bolesław V the Chaste and his wife St. Kinga, particularly for their contributions to the construction and reconstruction of the church and monastery after the devastation caused by the first Mongol invasion of Poland in 1241.
The Church was one of the earliest tall buildings in the city made of brick and sandstone. The original Gothic structure from the 13th century was consecrated before 1269 and expanded between 1260 and 1270. Only a few elements from that period, such as the ribbed vault, have survived. The presbytery was extended from 1401, resulting in the three-sided apse. Around 1420–1436, the cross-shaped central section with nave arcades was added, transforming the original straight chancel. This expansion was re-consecrated by Cardinal Zbigniew Oleśnicki in 1436. Despite enduring various calamities in 1462, 1476, and 1655, the Church of St. Francis of Assisi and the adjacent Monastery suffered its most destructive fire in 1850, resulting in the loss of written records of its consecration and priceless artifacts.
During the period of foreign partitions, the Franciscan Order in Poland faced great difficulties. By 1864, out of over 90 Franciscan monasteries, only 8 remained in the country, including the one in Kraków. The situation slightly improved after the Austro-Prussian War, when Austria granted Kraków a degree of autonomy following its own significant defeat in 1866. In 1895, the eastern part of the church was adorned with murals featuring floral motifs by Stanisław Wyspiański, a prominent figure of the Young Poland movement. Wyspiański also designed magnificent stained glass windows for the apse, which were manufactured at the Innsbruck foundry between 1899 and 1904. The renovated church was re-consecrated on 14 June 1908 by the Bishop of Kraków, Anatol Nowak, and was elevated to the rank of Basilica Minor on 23 February 1920.
The Chapel of the Passion, located within the Franciscan Basilica, houses the certified copy of the Shroud of Turin. This sacred relic is prominently displayed on the main altar of the chapel, allowing visitors and parishioners to closely examine it. The replica was blessed by Pope John Paul II at the Vatican on March 19, 2003, and was ceremonially unveiled by Cardinal Franciszek Macharski of Kraków on April 14, 2003.
The Shroud of Turin is a large burial linen measuring 4.36 by 1.10 meters (14.3 by 3.6 feet). It bears the reverse image of a man, widely believed to be Jesus Christ, who, according to tradition, was wrapped in the shroud before being laid in the tomb. Notably, the shroud prominently displays an imprint of what is believed to be the face of Christ at its center.