The church was built at the old trade route leading from Kraków to Sandomierz and further east to Ruthenia and Ukraine. Interestingly, in the Eastern Church, Saint Nicholas was venerated as the patron saint of Ruthenia and travellers. The earliest mention of the church dates back to the first half of the 13th century. A papal bull of 1229 mentions that it was owned by the Benedictine Fathers of Tyniec. In 1467, the Order donated the church to the Kraków Academy.

Originally a Romanesque building, it was refashioned to have a Gothic style after a fire in 1376. Burnt down during the siege of the city by the Swedes, the church was rebuilt between 1677 and 1682. Today's building has modest Baroque forms, apart from the Gothic, polygonal-closed and buttress-reinforced presbytery that conceals the remains of a Romanesque temple.

In the three-nave interior, among the furnishings dating from the 16th to 18th centuries, attention is drawn to the late Gothic altar-pentaptic with the scene of the coronation of the Mother of God, a superb work by Kraków painters from the late 15th century. The bronze baptistery from 1536 is also valuable, as is the late Renaissance white marble tombstone and the Gothic stepped portal in the sacristy.

In the area of the former cemetery surrounding the church stands the only unique Gothic roadside statue in Kraków from the 14th century, the so-called Lantern of the Dead. In the Middle Ages, such lanterns were mainly erected in front of hospitals, asylums, leprosaria and cemeteries, wherever one could seek treatment for infectious diseases. This lantern used to stand by the leprosarium at the Chapel of Saint Valentine in Kleparz, and was moved to the church grounds in 1871. Another unusual object is the Khachkar, or cross-stone. In Armenian culture, it is a reminder of important historical events and the dead. The Kraków Khachkar commemorates the Armenians who have lived in Poland since the 14th century. The monument is also dedicated to the victims of the genocide committed against 1.5 million Armenians in Turkey in 1915.

Mass is celebrated in the temple in the Armenian rite. The church is also the Sanctuary of Blessed Hanna Chrzanowska, whose confessional with reliquary is located in the side aisle.