The decision to invite Bernardines was made by king Casimir IV Jagiellon, while staying in Bydgoszcz castle during the Thirteen Years' War (1454–1466) against the Teutonic Knights.

[2] On December 5, 1480, Wloclawek's bishop Zbigniew Oleśnicki granted the erection of a Bernardine monastery in the city, only the third one in Poland after Kraków's and Warsaw's.

Its main official founders were king Casimir IV Jagiellon, Hińcza of Rogów, Jarand of Pomian and Bydgoszcz's Starost Jan Kościelecki.

A place was given to them with the consent of His Majesty the Polish King Casimir IV Jagiello, His Most Reverend Zbigniew Oleśnicki, bishop of Wloclawek.

[6] During the 17th century, the abbot, Paweł of Łęczyca, was an active supporter of urban decorations, founder of the extensive gardens of the monastery, which were ancestors of today's Bydgoszcz parks.

[2] On September 23, 1552, king Sigismund II Augustus granted permission for the reconstruction of the burned Bernardine church, as long as it was not taller than the neighboring castle, for military-defensive purposes.

In 1595, Dorothy of Spławski, the wife of Jan Kościelecki, the Starost of Bydgoszcz, had the chapel of the convent decorated with polychrome and three green rugs.

[3] The main altar, consecrated in 1559 and 1606 was covered with gold in 1760-1770: it is dedicated to the Holy Trinity, Mary of Nazareth and to several saints (Francis of Assisi, Bernardino of Siena, Louis and Bonaventure).

Until the end of the 18th century, the crypt was used to bury religious members of the Bernardine Monastery, along with regular people who deserved to be honored by the convent and the church.

In 1817, the Prussian authorities carried out the dissolution of the monastery, but the expropriation per se of the church only took place after the death of the last monk, Father Nagabczyński in 1829.

The last Polish chaplain of the garrison church, Father Wiktor Szyłkiewicz, was arrested and shot by the Nazis in September 1939; his grave is now in the Cemetery of Bydgoszcz Heroes.

The cylindrical church tower is in the south-western corner; it comprises a partially-embedded staircase and two octagonal upper storeys topped by a neo-gothic brick flèche.

Adjacent to the church stand the remaining buildings of the former Bernardine Monastery and the chapel of Saint Anne, built at the turn of the 16th and 17th centuries.

In 1967, archaeological excavations in the south of the church revealed the foundations of the Loreto chapel, the remnants of the cloister galleries and a former municipal water oak pipe from the 16th century.