The idea of founding the monastery dates to merchants (H. Huxer, G. Kruse, H. Swalbart) of Tallinn of around 1400. In 1407, two monks from the Vadstena Abbey arrived to Tallinn to counsel the merchants. First permit to break dolomite to gather building material for building the complex was acquired in 1417. Convent was constructed under the supervision of the architect Heinrich Swalbart. The main church of the monastery was consecrated on August 15, 1436 by the Bishop of Tallinn Heinrich II. During its heyday Pirita Convent became the largest Catholic monastery in Livonia. However, during Livonian war Pirita Convent was attacked by the Russian troops under leadership of Ivan the Terrible in 1557. They sacked the monastery, looted its riches and burned it down. Pirita Convent was abandoned since then, but adjacent lands were used for the cemetery by the locals.
Several of the merchants who had originally proposed the monastery later became its monks.