The Conservatori Riuniti di Siena dates back to 1580, when Sienese Domenico Billò, supported by many Sienese citizens, including nobleman Aurelio Chigi, founded the Congregazione delle Povere Abbandonate in Via Fieravecchia (Porta Romana) to give shelter to destitute women.  
In 1593, after the death of Domenico Billò, Aurelio Chigi took charge of the institution, adding further impetus to the Congregazione. In that same year, the neighbouring Palazzo di San Galgano was bought and in 1601 the construction of the Church of St Raimondo al Refugio was started - a precious example of the 17th Century Sienese art and culture. Also under Count Aurelio Chigi, the Congregazione delle Vergini del Soccorso in Via del Refugio was founded, an organisation which gave shelter to young women from decayed aristocratic families until the end of the 18th Century.

In 1785, the Grand Duke of Tuscany, Pietro Leopoldo, changed the Congregazione into the Conservatorio di San Raimondo al Refugio, aimed at educating young noblewomen and giving shelter to members of many convents and congregations which had been closed down. In 1891, after the unification of Italy, a royal decree ratified a merger agreement between the Refugio i Conservatori di San Raimondo and another Conservatorio which had been founded through the reform of Pietro Leopoldo. The Regi Conservatori Riuniti di Siena, under the Italian Ministry of Education, was thus founded.

During the first half of the 20th Century, the Conservatori was divided into three sections under the same management: an elemetary school (L'Educandato), a boarding school hosting young girls studying at different schools in the city (Il Convitto) and rooms for Italian or foreing young or elderly women who had to spend some time in Siena for cultural reasons mainly (Il Pensionato). A number of rooms (Posti Chigi) were offered to elderly unmarried women free of charge. Afterwards, in collaboration with the Municipality of Siena, a secondary school with an annexed kindergarten was opened.
The jurisdiction of the institution was amended twice, first through the royal decree of 23rd December 1929 and then through the royal decree of 1st October 1931, which included the institution within a list of the Conservatori of Tuscany.

After a period of severe hardship mainly because of the consequences of the second world war, the agreements with the University of Siena - from the 60s onwards - provided the Fondazione with new opportunities for the future. Some properties belonging to the Conservatori were rented to the University and became seat of the new faculty of liberal arts and philosophy. The profits from the rent of the the Palazzo di San Galgano allowed the Fondazione to refurbish the rooms in Via del Refugio, which were dedicated to the institution’s boarding school, hosting young university students from all over Italy willing to study at the University of Siena.

The regulation n. 27 from 3rd February 2006 changed the former organisation into the Fodazione Conservatori Riuniti di Siena. The Fondazione entrusted the management of its residential facilities to the Scuola Superiore Santa Chiara, which holds the Scuole di Dottorato di Siena.