The construction of the basilica took place in multiple phases, commencing in 1340 and continuing until the middle of the 15th century. Its primary purpose was to serve as a monastery church, which is evident from its expansive grounds and the adjoining monastic cemetery. In 1404, King Władysław II Jagiełło bestowed the basilica to the Canons Regular of the Lateran, a congregation that he had invited from Kłodzko.
The church's interior is a captivating blend of Polish Gothic and magnificent Polish Baroque architecture, showcasing notable features such as a grand gilded Baroque high altar, a pulpit shaped like a boat (1750), and a majestic organ. During the 1655 Swedish invasion (known as the Deluge), the church fell victim to extensive looting and destruction by soldiers, resulting in the prevalent Baroque style seen in its current decor. Renowned as one of the most exquisite Baroque choir stalls in Central Europe, the church holds a special place of beauty.
The Basilica of Corpus Christi boasts the largest organs in Krakow. The primary instrument was constructed between 1958 and 1963, incorporating certain elements from an older organ dating back to the 1770s. It was designed with 83 pitches and comprises two sections: the main organ situated on the choir and the side organs positioned in the chancel. Together, these organs boast an impressive total of 5950 pipes and 25 bells. They possess the remarkable ability to perform compositions written with an echo effect. The captivating sound of the organs, positioned 70 meters apart, provides a truly unique and immersive auditory experience for the listener.