The Dominicans, led by St. Hyacinth, arrived in Krakow from Bologna in 1222. They were brought by Krakow's bishop, Iwo Odrowąż, who gave the Dominicans the partially wooden and partially masonry parish church of the Holy Trinity, transferring the parish to the new Church of St. Mary. On March 12, 1223, the church was consecrated.
The new Gothic church and Dominican monastery began to be built after the Mongol invasion in 1241. Initially, it was a three-aisled hall, which was later transformed into a basilica-style church in the 14th and 15th centuries. Until the mid-19th century, one of the characteristic features of the church's exterior was the masonry bell tower, standing freely in front of the church's façade at the junction of Stolarska Street. After the city fire in 1850, only the charred walls of the bell tower remained, which were demolished during the church's reconstruction. In 1876, a neo-Gothic narthex was added to the church's façade in place of the tower. It covered the Gothic, 14th-century main entrance portal, which was renovated in 1893, including the replacement of several damaged stone fragments.
The church's period of glory came to an end with the devastating fire in Krakow in 1850. The entire interior, except for some chapels, was burned, and the nave vault collapsed. Immediately after the fire, comprehensive reconstruction of the church began. The work lasted from 1850 to 1884 and was led by architect Teofil Żebrawski. The charred walls were so weak that a part of the threatening façade had to be demolished. Upon commencing the reconstruction, it was discovered that the lower parts of the walls and pillars were too damaged to support the weight of the new vault. Therefore, the pillars were temporarily supported by wooden props and tightened with metal hoops. From 1853 to 1854, the pace of reconstruction was very slow, but new stained glass windows by German artist Hübner were successfully brought in. The following year, construction work resumed, reinforcing the emerging walls and covering them with vaults supported by brick pillars, only faced with stone. After removing the supports from under the arches of the main nave vault, on the morning of April 12, 1855, a part of the vault and walls collapsed, damaging a neighboring house. This construction disaster stirred public opinion in Krakow. The policy of cost-cutting in material selection was especially criticized. In order to ensure proper control, a special conservation committee was established in 1856. After raising the necessary funds and clearing the rubble, the laying of new foundations for the pillars began only in 1858. Three years later, the side naves were roofed, and in 1863, the main nave was completed. The basic reconstruction work was completed in 1872. As a result, the appearance of the church underwent significant changes, which met with criticism from artistic circles. The sculptor Edward Stehlik was particularly vocal in his opposition. The activities of Prior Fr. Marian Pavoni, an amateur architect who arranged the interior and exterior in the spirit of Neo-Gothic, also faced numerous attacks. During this time, the current main altar, choir stalls, and confessionals were created. After the reconstruction, in 1884, the church was consecrated.
Since 1957, the church has held the status of a minor basilica.
On October 19, 2016, a funeral Mass and farewell ceremony for the film director Andrzej Wajda took place in the basilica.
In January 2018, a comprehensive renovation of the interior of the church began.
Today, the Church of the Holy Trinity is a triple-naved Gothic brick-and-stone temple, built in the characteristic pillar-and-scarp system of Krakow, with an elongated presbytery ending in a straight wall.
Next to the main altar, Prince Leszek the Black, who died in 1288, is buried in the church. The presbytery of the church also contains a bronze plaque of the distinguished humanist Filip Kallimach, who died in 1496 and was designed by Wit Stwosz.
The organ was built in 1890 by the Rieger Brothers company from Jägerndorf as opus 756. The instrument has 30 voices, a mechanical playing action, and a pneumatic stop action. It is a valuable and interesting example of romantic organ building, while still maintaining its original sound concept to this day.
St. Rose of Lima Chapel (Lubomirski) - built in the early 17th century on the site of the Gothic burial chapel of Pilecki (built in the late 14th century). It was founded by Sebastian Lubomirski and his wife Anna of Branicki; their portraits are located in tondos on the wall shields. The dome interior is filled with depictions of St. Sebastian, St. Stanislaus, St. Anne with the Holy Family, and the prophet Elijah; the niches contain statues of saints (Dominic, Stanislaus, Stanislaus Kostka, Czesław, Casimir, Jacek, Florian, and Adalbert). The chapel is closed by a 17th-century grille.
St. Thomas Chapel - built in the 15th century by the tailors' guild. It is covered with net vaulting. The furnishings include a neo-Gothic altar designed by Marian Pavoni with statues of St. Thomas, St. Casimir, St. Stanislaus Kostka, St. Anthony, and Albert with the painting of Thomas Dolabella depicting the school of St. Thomas Aquinas, as well as a Renaissance tombstone of Nicholas Bogusz, the starost of Krasnystaw.
Savior Chapel (Przeździecki) - erected by Mikołaj Edeling in 1368, later came under the care of the bakers' guild, and in the 16th century it passed into the possession of the Orlik family. After a fire in 1850, it was restored by the Przeździecki family. It is equipped with a neo-Gothic altar made by Edward Stehlik according to the design by Teofil Żebrawski.
St. Joseph Chapel (Szafrańcy, Provanów) - built in the 15th century by the cobblers' guild, later owned by the Szafrańcy family. The furnishings include a neo-Gothic altar designed by Marian Pavoni with the painting of Christ in St. Joseph's workshop by Jan Angelik Drewaczyński and a Mannerist tombstone of Prosper Provano, the salt mine supervisor of Wieliczka.
St. Dominic Chapel (Myszkowski) - founded in 1614. It is distinctive and easily recognizable as it features a gallery of the Myszkowski family inside the dome. This chapel is also easily recognizable from the outside as it is adorned with rustication. It was built using noble silver-black marble, the columns are of a delicate, muted pink color, and the white sculptures enhance its elegance.
Rosary Chapel - built in the years 1685-88 in the shape of a Greek cross with a dome at the intersection of the arms, on the site of the earlier 15th-century Annunciation Chapel. In 1668, a painting of the Virgin Mary of the Rosary, which according to tradition belonged to St. Stanislaus Kostka, was placed in the chapel. It is located in the main altar between statues of St. Pius V and Blessed Benedict IX. The walls and ceiling are covered with polychrome paintings repainted in 1820 by Teodor Baltazar Stachowicz and in 1875 by Walenty and Władysław Bąkowski. They depict the mysteries of the rosary, the coronation of the Virgin Mary, saints, and angelic choirs. The chapel also houses the tombstone of Stanisław Sołtyk by F. Pozzi, a painting of Madonna with Child in a silver dress, and a figure of the Sorrowful Christ from the early 16th century. Since 1983, the chapel has been the burial place of Teofila Sobieska, the mother of King John III Sobieski, and Marek Sobieski (brother of John III).
Zbaraski Chapel - founded by Krakow Castellan Jerzy Zbaraski between 1628 and 1633 as a family mausoleum. It was built on the site of the medieval Chapel of St. Catherine of Siena. The builders of the Zbaraski Chapel were the brothers Andrea and Antonio Catello, and the designer was possibly Constante Tencalla. Tencalla's design is indicated by the similarity of details to the facade of the Chapel of St. Casimir in Vilnius. The Zbaraski Chapel rises on a rectangular plan and is covered by an elliptical dome, which was unusual for its time. The interior is made of black marble. Opposite the entrance is an altar with a painting by Teodor Baltazar Stachowicz depicting the vision of St. Catherine of Siena. On both sides of the painting stand statues of St. Catherine of Alexandria and St. Catherine of Siena. On the right side of the altar is the tombstone of Jerzy Zbaraski, and on the left side is the tombstone of Krzysztof Zbaraski. The stucco work was done around 1632. The chapel is a fully independent and original work that does not have a direct prototype in Italy.
Saint Mary Magdalene Chapel (Małachowski) - built in the 15th century; in the 16th century, it was dedicated to St. John the Baptist and belonged to the Tęczyński family. Since 1884, it has belonged to the Małachowski family. It contains a neo-Gothic altar designed by Marian Pavoni with a painting of St. Mary Magdalene by Władysław Bąkowski, a painting of The Feast at Simon's House by Thomas Dolabella, and a funerary monument of the Małachowski family from 1884.
Crucified Jesus Chapel - built in the late 14th century with the foundation of Jan Ligęza, the castellan of Łęczyca. It was formerly dedicated to St. Stanislaus. In the 17th century, it was cared for by the masons' guild. On the arcade, there are fragments of Gothic murals from the late 14th century depicting St. Catherine of Alexandria and two prophets. The furnishings include a neo-Gothic altar according to the design of Marian Pavoni with a painting of the crucified Christ by Józef Simmler. Next to the altar is a neo-Gothic reliquary with the remains of Blessed Wit, a 13th-century apostle of Lithuania. Opposite the altar stands a marble funerary monument of General Jan Skrzynecki. Masses commemorating the Battle of Grochów are celebrated in the chapel.
Saint Hyacinth Chapel - it houses the remains of Saint Hyacinth in a late Baroque tomb placed on the altar. The altar was made between 1695 and 1703 by Baltazar Fontana. The same artist decorated the chapel with stucco work around 1700. The walls were painted with polychrome by Karol Dankwart at that time. The chapel also contains scenes from the life of Saint Hyacinth painted by Tomasz Dolabella. The chapel is closed by a gate from the mid-18th century.