The exact year of the foundation is not known. The abbey was founded by King Inge I of Sweden and Queen Helena[1] on the orders of Pope Paschal II, which gives a date range for the foundation: Paschal became pope in 1099; the date of Inge's death is disputed, but probably occurred around 1105 or a little later. In the following decade King Inge the Younger and Queen Ulvhild made large donations to it.

Vreta Abbey was a house of Benedictine nuns until 1162, when it was turned into a Cistercian nunnery. The first Cistercian abbess was Ingegerd, sister of Charles VII. A second sister, Helena of Sweden, widow of Canute V of Denmark, entered Vreta as a nun after being widowed in 1157, and other members of the Swedish and Danish royal families were also here. It was a prestigious establishment, thought to be the burial place of the kings Inge the Younger, Filip Halstensson and Ragnvald Knaphövde. It served as a school for daughters of Sweden's ruling families and nobility. Vreta Abbey has entered folklore as the scene during the 13th century of a number of prominent abductions of girls for marriages disapproved of by their families[2].

Vreta was the mother house of Askeby Abbey near Linköping, Riseberga Abbey in Närke and Solberga Abbey in Gotland.

The buildings burned down in the early 1200s, but were rebuilt, and a new church was dedicated in the presence of Magnus Ladulås and Queen Helvig of Holstein in 1289.

After 1527, as a result of the Reformation the abbey was forbidden to accept any new novices, but was otherwise treated very leniently. It continued in use as a school for daughters of the nobility and a retirement place for old noblewomen, and in 1529, the King allowed the last abbess, Sigrid Botholfsdotter (d. 1538), to buy it, and its activities continued undisturbed. In 1536 the King Gustav Vasa gave the abbey and its assets to his Roman Catholic mother-in-law Ebba Eriksdotter Vasa, the mother of the Queen consort Margareta Leijonhufvud, also a Roman Catholic; Ebba Eriksdotter spent her last years here and died in 1549. There were still nuns here in 1562, and the last two of whom, Brita Gisledotter and Kirstin Månsdotter, died in 1582.