The consecration of the enlarged church of the Holy Spirit took place on 21 September 1645, the ceremony was chaired by suffragan bishop Piotr Mieszkowski from Włocławek, assisted by the abbot of the Cistercian abbey of Koronowo.

New elements in the interior have been put inside: in 1651, a grid iron separating the chancel from the nave, and in 1661 a tombstone plaque of Sophia Smoszewska -founder of sisters' monastery in Bydgoszcz.

In 1730, funds donated by Helen Zkoraczewską Złotnicka helped to rebuild all the windows in the church, and in 1746 a porch with 2 entrances was added (no traces today).

In a detailed visit made in 1760, Livonian bishop Antoni Kazimierz Ostrowski reported that the church was all in brick and covered with Polish tiles.

Items observed included: church bells, missals, books, monstrance, chalices, cruets, crosses, candlesticks, lamps, dresses, votives, chasubles, covers, albs, surplices and belts.

The buildings was transferred to the hands of the city, and by decision of Eduard Heinrich von Flottwell, governor of Grand Duchy of Posen, church worship was to be abandoned and the interior to be used for other purposes.

Then an alcoholic beverages store was installed: part of the western chancel (with the former gallery) was isolated and refitted, an opening was made through the southern wall for the warehouse.

Initially, the 1897 project should take a modest form but eventually urban architect Carl Meyer, with the help of Prussian conservator J. Kothe, changed the design, using 1844-drawing of Ferdinand von Quastof.

Idea was raised to transform the ex- sacred buildings into a prison: the members of the Historical Society of Netze District strived to grant sanctuary for museum purposes.

[7] During World War I, the basement of the chancel has housed emergency medical service (Polish: Pogotowie ratunkowe), in the nave were stored benches and postal supplies.

After renovation, the church interior has gained new equipment, including an altar from a Poznań workshop Roman, new benches, stalls, kneelers, confessional s and a pulpit realized using older sculptural elements.

The ceremony has been conducted by Consecrated by Cardinal Edmund Dalbor, Archbishop of Gniezno and Poznań, assisted by Antoni Laubitz, and the pastor of the parish church in Bydgoszcz, brother Tadeusz Skarbek-Malczewski.

[7] On 16 November 1925 another ceremony of consecration occurred to "re-grant" St. Clare's church to the Assumption of the Blessed Virgin Mary, celebrated by suffragan bishop of Gniezno Antoni Laubitz.

This work included, inter alia, partial roofing, renovation of façade near the summit, changes to the window openings and veneering of the facade.

In 1952, while scraping out internal plaster ], relics of four embedded crosses have been revealed in the chancel (Polish: Zacheuszek), probably from the time of the first consecration of the church in 1645.

Its return was preceded by many years of efforts from the rector of the church, brother Gierzyński, supported by the written consent of Primate of Poland Stefan Wyszynski.

[7] In 1971, due to the need to modernize the streets in downtown Bydgoszcz, an option discussed was shifting the church of St. Clare to the place of the building of the monastery, which would be demolished.

[7] In 1991 began the restoration work of the main altar, and the plaster covering of the chancel walls and vaults, removing old stucco from the 1920s and revealing original primary colors.

This church harmoniously combines elements of different architectural styles, Gothic, Renaissance and Baroque[9] The oldest walls in the northern part of the chancel date from 1582.

The nave of the church is covered with wooden, polychromed ceiling from with the first half of the 17th century, a complex of 112 coffers adorned with painted rosettes and symbolic characters.

It is divided into cornices and arcades and decorated with volutes, obelisks and globes[3] On the north-west corner of the church structure stands a circular tower, with confers a sturdy and unusual silhouette to the whole building.