The construction of a new church in Gothic style began here after the Tartars invaded in 1241. Another reconstruction at the turn of the 14th century gave the building a basilica character. Until the mid-19th century, a brick tower with a belfry still stood in front of the temple, facing Stolarska Street. Unfortunately, it met its end in the mid-19th century. In 1850, a fire broke out in the town, consuming the church bell tower and almost the entire church interior and causing the vault of the nave to collapse.

The temple rebuilding started quite quickly but slowed down after a while, and eventually, part of the rebuilt walls collapsed again. After this event in 1858, the reconstruction process began again. Work was finally completed in the second half of the 19th century, and the reconstructed church was consecrated in 1884. Since 1957, the church has had the dignity of a basilica minor.

The Basilica of the Holy Trinity of the Dominican Fathers is known as the centre of the cult of the patron and founder of the Polish province of the Dominicans and of the first monastery of this congregation in Poland, St Jacek Odrowąż. His remains rest in the chapel above the church sacristy (entered by a staircase above the left side aisle), where the saint's monastic cell was once located. Adjoining the right-hand side nave of the church is a chapel with a miraculous image of Our Lady of the Rosary. It was created in Rome and is a copy of the famous painting of Our Lady from the Roman church of Santa Maria Maggiore. The Kraków image was crowned with papal crowns in 1921. The Feast of Our Lady of the Rosary is celebrated on 8 October, while the memorial of Saint Jack falls on 17 August.