The first church was built from wood along with the city hospital of the Holy Spirit in the 14th century. This was probably the first hospital of its kind in the Mazovia region (located beyond the walls of Old Warsaw, founded by Duke Janusz the Elder and handed over to the city in 1388).
Next to the existing small church of the Holy Spirit, councilors and citizens of Warsaw wanted to establish a hospital. For this purpose, it is said that Mikołaj Panczatka donated a third of the denarii from butchers' shops, stalls, and marketplaces to the church, which amounted to a third of the Warsaw bailiwick. The hospital was referred to by various names in official documents: a guesthouse for the poor (1425), oraculum (chapel) of the Holy Spirit, connecting the small church with the hospital (1473), xenodochium (a room or guesthouse in a monastery for temporary accommodation of guests or pilgrims), and eventually, considering the small church as an "addition" to the hospital, it was called a cenobium (monastery) (1473). The fact is that the parish priest of the Holy Spirit served as the administrator (provisor) of the hospital. The first known parish priest of the church by name was Jędrzej Pronobis in 1473. The chronicles talks more about the Hospital of the Holy Spirit than about the church itself, and practically the majority of privileges received (e.g., from King Sigismund the Old and Queen Bona) were related to the hospital. Parish priests are also mentioned: Jan Szeliga (1574), Wojciech Pruszczyński (1579), and Wojciech Badowski (1633). In 1629, the Bishop of Poznań, Maciej Łubieński, merged the parish of the Holy Trinity, whose buildings were given, by the king's command, to the Bridgettine Sisters (today, there is no longer this church and monastery buildings; they were located on Nalewki Street, opposite the exit of Bielańska Street) with the parish of the Holy Spirit.
The temple suffered during the Swedish Deluge. By a resolution of the city council on August 22, 1664, the church, along with its income, the title of the parish, and all its possessions, benefits, and conveniences, was given to the Pauline Fathers.
In 1699, the cornerstone was laid for the new church, which was built between 1707 and 1717 in the Baroque style according to the design of Józef Pioli and Bellotti. One of King Augustus the Strong's friends, the voivode of Chełmno, Rybiński, who was invited as the main guest for the ceremony of laying the cornerstone, allocated a significant amount of 40,000 złoty for the construction, which was substantial for that time. However, the majority of the funding for the construction came from the Brotherhood of Jesus of the Five Wounds associated with the church, mainly comprised of Warsaw citizens. The driving force behind the construction and decoration of the church was Prior Innocenty Pokorski (during the second Swedish invasion, he held the position of prior at Jasna Góra). Finishing works and the construction of altars continued until 1746, when the Chapel of the Most Holy Virgin of Częstochowa was built. Under the supervision of J. Bartoszewicz.
The chronicler notes that on March 12, 1800, there were 12 priests at the time, and the novitiate was not present, but there was a theological study in the monastery, with two professors and four students who were studying speculative theology and dogmatics, as well as practicing the resolution of conscience issues and knowledge of church ceremonies.
In January 1807, Napoleon Bonaparte's troops approached Warsaw, and the monastery was taken over as French barracks. And although the Pauline monks briefly regained the monastery after the war (under the leadership of Father Teodor Fortuński), in July 1819, the administrating bishop ordered his priests to be relocated to Częstochowa within four weeks at the latest, leaving all equipment behind, as they were responsible for any damage... and in August, the church was handed over to the German Brotherhood of Saint Benno. Subsequent rectors had German surnames, suggesting their German origin, such as Lűdicke, Amman, Gueldre, and Ballach.
In the Pauline monastery, on September 22, 1825, the main seminary was opened, which, combined with the university's theological faculty, formed a single entity. The first rector of the seminary was Father Żółtowski, followed by Father Jan Onoszko until 1836, a canon from Mohylew. In that year, the seminary was elevated to the rank of academy and moved to the Franciscans. The remaining part of the monastery was rented out as residences. The seminary's place was taken over by a district and later a county school, and finally, in 1852, a wall was built to separate what was meant for the church and what was for public use.
After the January Uprising in 1863, a figurine of the Virgin Mary was placed in front of the church.
During the Warsaw Uprising, the church was destroyed by the Germans due to bombing, and dozens of people died in its underground chambers. After the war, the damage to the building was estimated at around 50%. The Pauline monks returned to the church and monastery in 1948. The reconstruction was completed in 1956.