The small temple stood on the road to Wawel Hill, near the ‘Spring of St Adalbert’.The present Romanesque church was erected in the early 12th century. The church has been rebuilt several times, and it now combines Romanesque, Gothic and Baroque features. Of the various Romanesque elements, the stonework has been preserved: the moulded windows, the portal and part of the stone block wall. 

The earliest written records of the church date back to the 16th century, and the existence of a building on the site was confirmed by architectural research and archaeological work carried out in the 19th and 20th centuries. The first temple (10th–11th century), made of wood, consisted of a small presbytery, nave and vestibule; another building built on top of the previous one in the second half of the 11th century also had a wooden floor. Traces of a cemetery found near the church also date from that period. The stone building, built atop two previous ones, was erected at the turn of the 10th and 11th centuries and then rebuilt in the 12th century, and these Romanesque walls remain admirable to this day.

Thanks to Bishop Piotr Wysz Radoliński, the church became a university prebend in 1404. In 1453, at the invitation of Cardinal Zbigniew Oleśnicki and King Casimir IV Jagiellon, the then highly acclaimed preacher Saint John Capistrano, a Franciscan friar and founder of the Observant branch of his order, popularly known as the Bernardines, gave his sermons here.

The subsequent reconstruction of the church did not occcur until the 17th century. Due to the rising level of the market pavement over time, the church was raised by about 4 metres (the Romanesque floor by more than a metre) and reinforced with bricks. It was then that the distinctive circular windows. The presbytery was covered with a barrel vault and the nave covered with a cupola. Henceforth, instead of the south side, the church is entered through an entrance carved into the west wall. A small sacristy was added to the north, and a little later, on the south side, a wooden chapel was dedicated to St John of Nepomuk. When the building was restored in the 18th century, the wooden sacristy was bricked up, the church was decorated with paintings by Andrzej Radwański, and the side chapel was renamed the Chapel of Blessed Wincenty Kadłubek. New altars, consecrated by Bishop Michael Koźmin, were also installed (including the main altar with 17th–century paintings of Our Lady with Child and Saint Tekla and with statues of Saint Adalbert and Saint Stanislaus), as well as the choir and a Baroque confessional.

With the outbreak of the Kraków Uprising (1846), a field hospital for the wounded and a prison were set up in the Church of St Adalbert. Subsequently, the landlord at the time ordered a significant rrenovation, which resulted in new plasterwork, with the Romanesque walls, including the soaring window in the chancel, remaining exposed. Stone bollards with chains surrounding the church were then set up.

Between the wars, it was possible, among other things, to dry the foundations, repair the Romanesque plasterwork and add a porch connecting the presbytery with the chapel of Blessed Vincent. At the same time, conservation work and archaeological investigations were underway.

The last remarkable changes were made in the 1960s. The two Baroque altars and pulpit were removed, and the cracked paintings in the dome were replaced with works by Eugeniusz Czuchorski. At that time, the building was divided into two levels: the upper level was now the church, while the lower level was an exhibition on the underground history of the Market Square. It was there, at an exhibition organised by the Archaeological Museum in Kraków ( Link to the description of the Church of St. Adalbert in Kraków), that we can now admire a reconstruction of the first wooden church dedicated to St Adalbert, the foundations of its Romanesque walls and numerous artefacts found by archaeologists.

Since 1949, the Church of St Adalbert has been a rectoral church.