The church was established by Piotr Skarga for the Jesuits of Cracow. The cardinal Jerzy Radziwiłł was the main founder of the church. The corner-stone of the church was laid in 1597. Several architects supervised the construction works until 1633. It is said that Giovanni de Rosis, Giovanni Maria Bernardoni and Giovanni Battista Trevano were the ones who had the biggest impact on the shape of the church. It is a great example of a temple designed after the Baroque churches of Rome. It was the first project in Poland done on such artistic scale. Jesuits wanted the church to be located in an important place in the town. Originally they planned it on one of the corners of the Main Market Square. Finally it was decided to build the temple in Grodzka Street, along the Royal Way.
We have a nice view on the church and its surroundings from Marii Magdaleny Square. It appeared as late as 1945. Earlier at this site there was a Gothic Church of Mary Magdalene and after it was pulled down, a tenement house. It means that in the past the façade could be seen only from an angle. In order to expose it the whole building was moved back from the street. The triaxial two-tiered façade is decorated with stone pilasters and a moulding. Between them there are statues of saints. There are interesting buildings around the square itself. Along the southern side there is a large house called 'malarnia' (painting house), which housed the Painting School during the period of the Republic of Cracow. Along Kanonicza Street we can see the classicistic façade of the former Stanisław Wyspiański Museum. From the North the square is closed by the side wall of Collegium Iuridicum. In the middle of the square there is a new monument of the preacher and a priest Piotr Skarga. His tomb is in the crypt of the Church of SS Peter and Paul.
The monumental façade of this Baroque church is divided by five axes. It is ordered by the flat pilasters and the large moulding of the entablature in the Colossal order. Above the entrance in a square plaque there are initials IHS, the emblem of the Jesuits. On the left behind the trees there are the buildings of the former Jesuit college — today the Collegium Broscianum of the Jagiellonian University. On the right from behind the greenery we can see the silhouette of the Church of Saint Andrew. In front of the church there is a fence designed by Kacper Bażanka with stone figures of the twelve Apostles in expressive poses.
The main nave, the transept and the choir with a semicircular apse form together the interior. On the sides of the wide nave there are three aisles. The interior has barrel vault supported on arches. At the crossing of the nave and the transept there is an elliptic dome topped with a lantern. Monumental stucco pilasters and mouldings give the interior classical character. The decorations reach the highest point in the choir. We can see here a late-Baroque altar by Kacper Bażanka from 1738. In the central part of the altar there is a 19th-century picture Wręczenie kluczy św. Piotrowi (Granting the Keys /to Heaven/ to Saint Peter). Above it we can see the scene of the apotheosis of Saint Paul. Stucco decorations in the concha of the apse were done by G.B. Falconi by the design of G.B. Trevana.From the choir we enter the crypt. There were buried the meritorious bishops and priests with the great moralist Piotr Skarga (died in 1612) among them. In the transept there are side altars from the first half of the 18th century. We can also admire the tombstones which appeared on the walls during the centuries. The family grave of Rohoziński and Michałowski with the Ecce Homo figure is situated in the northern arm of the transept to the left from the altar. In the southern part our attention is caught by classical tomb in the shape of a pyramid of the Bartsch family from 1827. On the other side of the altar we can see the marble statue of Maurycy Poniatowski from 1878. In this part of the transept on the wall there is placed a late-Baroque tombstone of the Branicki family. Kacper Bażanka was the author of this huge composition of sculpture and painting. Early-Baroque pulpit is placed at one of the pillars of the transept.