The idea of founding the Bridgettine Convent originated from the merchants of Tallinn around the year 1400. In 1407, two brothers from the Vadstena Monastery in Sweden arrived to advise on establishing the new sacred site. However, it took about a decade to start building the convent complex, as it was not until 1417 that the first limestone quarry permit was obtained.

Some of the merchants who initiated the idea of founding the monastery became brothers of the new monastery. One of them, Hinrich Swalbart, led the construction efforts. The central structure of the convent, the church, was consecrated in 1436. Construction continued on both the sisters' and brothers' sections of the monastery until the early decades of the 16th century. The progress of the construction was likely influenced by a shortage of funds, and the western wing of the nunnery was probably not completed according to the original plan. The building site was donated to the monastery by the Livonian Order.

The Pirita Convent church (internal dimensions 24×56 m, western gable height 35 m, area 1360 m²) was impressive in both size and volume. The simple convent church had a long, multi-vaulted rectangular floor plan, divided into two equal parts—a convent church and a public church—by a mid-screen, the former accessible only from the monastery, the latter also from a roadside portal. During major holidays, when the church could not accommodate all visitors, sermons were held from an exterior pulpit, the opening of which can be seen in the facade’s upper part. The sisters' choir was located in the northern aisle, to the left upon entering from the portal. Beneath the sisters' choir were five confessionals.

According to the rules, the church was to have 13 altars, each bearing the name of an apostle, so that each priest had his own altar and apostle. Additionally, there were several side altars, including one dedicated to Saint Bridget.

Pirita convent was also an international pilgrimage site. Guest rooms were supported against the church's northwest outer wall.

Both the male and female monastic living quarters were centered around a quadrangular courtyard, which served as a recreational area surrounded by residential buildings. Encircling the courtyard was the “eternal path”—a cloister, a place for gathering and walking. Both the male and female monasteries had separate entrances to the church, and in the church, brothers and sisters had their own separate areas for prayer.

Pirita convent operated for nearly 175 years during the Middle Ages. Its demise was hastened by the Livonian War (1558–1583) and a fire in the spring of 1564 that devastated the convent's economic center. In the early years of the Livonian War, the Tallinn Council debated demolishing the convent for strategic reasons, but this was not carried out due to opposition from the knighthood. The convent suffered a severe blow in 1577 when the forces of Russian Tsar Ivan IV heavily plundered it during the siege of Tallinn. In addition to the convent, the nearby monastic settlement, used by the convent's secular workers and fishermen, was also destroyed.

The masterless ruins were occasionally used up until the Great Northern War (1700-1721), after which the ruins were emptied again. The church space, with its high walls, presumably too cumbersome for raiders to dismantle, remained almost untouched.

The first systematic archaeological excavations on the Pirita convent grounds began in 1934. These early excavations already revealed impressive finds, with many more added during renewed excavation work in the early 1960s. The total number of finds is awe-inspiring—nearly twenty thousand detached finds were discovered above the church and the nunnery’s enclosure buildings, dating from the 15th century to the 20th century. Among the finds were exquisite architectural carved stones, fragments of ceramic vessels, even golden rings worn by the nuns as mandated, and more.

Several extensive excavation and conservation works were also conducted on the medieval monastery grounds at the end of the last century, partially uncovering and conserving the foundation of the old nunnery’s infirmary and the boundary wall that protected the monastery from the north.

The motherhouse of the Bridgettine Order was consecrated in 1384 in central Sweden at Vadstena; Pirita convent on the eastern shore of the Baltic Sea was the order's third daughter monastery.

The church gathered seven times a day to sing praises to God with King David’s songs; each week, the entire Book of Psalms, 150 psalms, was sung through. It might not be an exaggeration to say that the sisters of Pirita Monastery formed Estonia’s first large female choir, and the monastery’s grand beautiful church was the largest concert hall in the Land of Mary, where performances occurred seven times a day, year after year.

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The sisters of Pirita convent also engaged in reading and meditation, as well as household chores and crafts, while the brothers could additionally preach in other churches. The sisters never left the monastery, and after their deaths, they were buried in the monastery church. Today, 15 tombstones that were originally on the floor of Pirita Monastery's church are affixed to the walls of the church ruins.

The founder of the order was a Swedish woman— in 1346, the Swedish noblewoman Birgitta Gudmarsson (née Birgersdotter) wrote the constitution or rule of a new spiritual order (Latin: Ordo Sanctissimi Salvatoris, Order of the Most Holy Saviour) based on her visions, which was confirmed by the Pope in 1370.

A distinctive feature of this order was the double monasteries, where the branch of the male members also submitted to the abbess. The spiritual ideal was the first Christian community in Jerusalem, which had as many priests as there were apostles, 13, and 72 disciples, with the Virgin Mary as the model for the sisters and the Apostle Peter for the brothers.

In the Middle Ages, the order had dozens of monasteries. According to Saint Bridget's rule, a double monastery could have at most 85 sisters and 25 brothers (of which 13 were priests, 4 deacons, and 8 lay brothers). The monasteries were situated on opposite sides of the church, which was common to both.