The first wooden church, founded by Bishop Pełka in the 12th century, was taken over in 1244 by the Order of Spiritualists, who ran a hospital. When recalling the church's history, one cannot ignore the fire of 1528, which consumed the entire interior and part of the building's structure. Then, the presbytery vault collapsed, but it was quickly rebuilt.

The church is a classical, very simple Gothic building dating from the late 13th or early 14th century. It consists of a square brick nave and a smaller rectangular stone presbytery. Above the west façade is a six-storey square tower, the ground floor of which is adjoined by two chapels. The church underwent two major renovations in the second half of the 17th century and after the end of the 19th century.

It is interesting to note that Stanisław Wyspiański worked on the reconstruction of the polychrome. The artist wanted to complete the missing parts of the paintings with his frescoes. Unfortunately, he could not realise his ambitions and, angered, ended his collaboration with the architect Tadeusz Stryjeński.

Noteworthy are the chapels adjacent to the tower, the Chapel of St Andrew dating back to the 16th century and the Chapel of Our Lady of Loretto from 1642. Inside the church, an unusual nave vault is supported by a single central pillar symbolising the biblical Tree of Life. On the right behind the entrance you can see a lavabo (priest's basin) from 1581, dating from the Church of the Holy Spirit, used today as a stoup. The main altar, dating from the early 18th century, features a 17th-century cross. To the left of the nave is the altar of St Anne with a central painting of the Teaching of Mary from around 1650. To the right is the altar of the Virgin Mary, dating from 1630. The Chapel of Saint Sophia contains a unique late Renaissance confessional, one of the oldest preserved in Kraków, from the end of the 16th century, and a baptismal font from 1423.

Until 1891, the church was surrounded by the parish cemetery, the monastic buildings of the Order of the Holy Spirit and the Hospital of the Holy Spirit. Neither the cemetery nor the buildings have survived to this day.