The church was built at the same time as the monastery in 1683–1694 at the initiative of King Jan Sobieski, apparently as a votive gift for victories in the battles of Khotyn and Vienna.
The Bishop of Poznań, Wężyk, granted canonical permission for the foundation of the church on December 27, 1681. The king bought a site on Honey Street. Initially, a small chapel was built (in 1682), where the order's brothers began to hold prayers, and it quickly became popular among the residents of Warsaw. The following year (July 11), the king ordered the issue of a location diploma for the foundation of the monastery. The first stone for the construction of the church was laid on July 23, 1683, before the dispatch of troops to Vienna. At the festival of the laying, Jan Sobieski himself, Queen Marysieńka, their sons, the Apostolic Nuncio Opizo Pallavicini, the Archbishop of Ephesus, Bishop Wężyk, senators, hetmans, ministers, and many Warsaw residents were present. By the king's order, instead of "Christo Redemptori Joannes III. Polon. Rex …", the words "Christo Triumphatori Joannes III. Polon. Rex …" were carved on the stone.
In the spring of 1686, Father Paul from Imola began the construction of the monastery according to the design of the Italian architect Isidoro Affaitati (the younger). Because the project, in its grandeur and splendor, contradicted the king's instruction to build a modest monastery, the previous architect, Augustyn Locci, created a new design, and the city architect, Karl Ceroni, was appointed as the overseer of construction. In May 1688, a plot intended for a farm and gardens, stretching from the church to the palace of Bishop Zbański, was additionally purchased. The final project was apparently by Tylman van Gameren.
Pope Innocent XII, in a brief dated December 1, 1691, included the Warsaw and Kraków monasteries of the order in the Tuscan province and approved a novitiate for 12 Poles. Father Francis Arretsi was appointed the new General Commissar of the Capuchins in Poland.
The church was consecrated on October 11, 1692, but its construction was only completed in 1694. The bell for the church was transferred from the Vilanovian clocks. The king also wanted to build a lower church, but geological conditions did not allow this plan to be realized, and the basement was designated for the crypt.
By 1738, there were about 50 Polish monks in four monasteries in Poland, and the Vatican entrusted their care to the Czech province, and Benedict XIV (on October 5, 1754) raised the Polish custody to the rank of a province, which Clement XIII declared independent in 1761.
On June 17, 1983, during his second trip to Poland, the temple was visited by John Paul II. The Pope prayed before the Most Holy Gifts, and also before the urn with the heart of Jan Sobieski in the Royal Chapel.
The interior and exterior of the church did not entirely correspond to the image of poverty with which it was supposed to be associated, as belonging to the Capuchin order. Its facade was divided by Tuscan pilasters on a high base and crowned with a triangular pediment, decorated with the Sobieski coat of arms, Janina's. Modest, but at the same time majestic, such a facade was subsequently repeated in the construction of Polish provincial churches.
On the facade, there is a memorial plaque dedicated to Yuriy Krizhanich.
Unlike other buildings of the order, the church was distinguished by its impressive size, a high nave with three bays instead of the usual two, and galleries that encompassed the entire interior space. Deep lower chapels are located on both sides of the nave. The narrow presbytery, equipped with two side rooms, behind which the choirs are located.
In the church itself, the walls are treated with pairs of Tuscan pilasters and outlined with a wide double cornice. By order of the king, they were decorated with a mosaic, for which special permission from the pope was required.
The main altar features paintings of the Transfiguration of the Lord and St. Adalbert by Szymon Czechowicz. On the cyborium is an oil painting of Christ's head wearing a crown of thorns by an unknown artist. Above, under the vault, over the altar, is a shield with the Sobieski coat of arms – Janina, supported by angels. On the pillars of the main altar, to the right is the altar of St. John Nepomuk with an oil painting of the saint, and to the left is St. Fidelis (Marco Roy), the first Capuchin martyr, also with a painting.
The next altar on the right side is the Altar of the Immaculate Conception of the Blessed Virgin Mary, with an image of the Virgin crowned with silver and gold-plated crowns. Previously, a mosaic painting of the Annunciation of the Blessed Virgin Mary was in the altar.
Next is the altar of St. Anthony of Padua, also with an oil painting of the saint.
The third altar on the right side features the Lord Jesus, with a figure of Him on the cross carved from bone, behind glass, of beautiful craftsmanship.
On the left side, there were only two altars: St. Francis of Seraph with a painting of the saint from the Vatican gallery, a gift from Princess Czartoryska, sister of Stanisław August, and the altar of St. Felix, a Capuchin, with a wax statue of the saint behind glass, famous for numerous miracles.
Two chapels were on the left side of the temple.
The chapel, formerly called royal and after the deposition of the king's heart (June 26, 1830), named the Chapel of John III, with an altar and a painting of the blessed Angel of Acri by the Warsaw painter Gładysz, moved from the church of St. Anne (Bernardines). In this chapel are entombed, in a sarcophagus (personally by Henryk Marconi), the entrails of John III preserved in a lead box and the king's heart placed in a monument by Bishop Adam Prosper Burzyński in a silver vessel shaped like a heart and bound. A bust of John III, made of white marble, is the work of Ludwik Kaufmann. This sarcophagus is located on the right side of the altar, while on the left side is the sarcophagus of August II the Strong with a gray marble urn containing the king's remains. The chapel was oval with two windows, and glass doors separated it from the church.
The second chapel of St. Cajetan (formerly the "Brühl chapel") has an altar painting of the saint by an unknown Italian painter, purchased by Princess Czartoryska from the former Theatine monastery (located at Długa Street in the house of Chancellor Joachim Litawor Chreptowicz).