The association of the Conservatori Riuniti di Siena, also known as "Refugio", dates back to the end of the 16th Century. Back in 1580, Domenico Billò, a Sienese citizen, a second-hand dealer, opened the doors of his house in via Fieravecchia to young destitute women and set up the Congregazione delle Povere Abbandonate. Among the main supporters of the congregation was the Sienese nobleman Aurelio Chigi, who took charge of the Congregation after the death of Billò on 12th July 1593. Chigi added great impetus to his predecessor's endeavour to protect young women in need.

In that same year (1593), Chigi bought the nearby Palace of San Galgano, named after the monks of the Abbey of San Galgano, and founded another Congregation - the Congregazione delle Vergini del Soccorso, which gave shelter to young women from decayed aristocratic families. In 1601, following the will of Aurelio Chigi, the construction of the Church of St Raimondo al Refugio began. The Church still contains a rich heritage of precious works of art - Sienese paintings, sculptures and minor arts from the 17th Century. The two Congregations, Povere Abbandonate and Vergini del Soccorso, were based in neighbouring buildings for nearly seventy years.

In 1674, the Povere Abbandonate - the young women not belonging to noble families - were moved to the nearby Monastery of San Girolamo. Thanks to the administrative rigour of the institution, the strict enforcement of the Founder's rules and the efficient education system within the congregation, several citizens, noblemen and members of the high-ranking clergy appreciated and showed their generosity towards the institution. Through the following  decades, generous donations and endowments raised the value of the institution's heritage. A considerable change was brought about at the end of the 17th Century, when the Grand Duke of Tuscany, Pietro Leopoldo, closed down many convents with the aim of transferring the role of educating young people to non-religious institutions. Following the enforcement of Pietro Leopoldo's decree, members of other convents, especially from the Convent of Monna Agnese, moved to Refugio and rooms from the neighbouring Convent of Santa Monaca were assigned to the newcomers. Another change introduced by the Grand Duke involved the name of the institution, which was changed from La Congregazione delle Vergini del Soccorso into Conservatorio di San Raimondo al Refugio. The new mission of the institution was to educate the young noblewomen. The educational programs included: Italian, mathematics, history, geography, music, poetry, dance, sewing, embroidery and many more, but also notably three foreign languages, French, English and German. On 4th January 1891, a royal decree ratified the unification of the Conservatorio di San Raimondo al Refugio and the Convent of Santa Maria Maddalena (which had been set up after the reform of Pietro Leopoldo) under the new name of Regi Conservatori Riuniti di Siena and under the jurisdiction of the Italian Ministry of Public Education.

The jurisdiction of the Public Institutes for Female Education was amended after the signing of the Patti Lateranensi, through the royal decrees of 23rd December 1929 and 1st October 1931. The latter contains a list of the Conservatori of Tuscany, among which there is also the Conservatori Riuniti di Siena. 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 house 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. In 1928 the institution underwent a further enlargement when the Convitto Comunale femminile dei Tufi, a boarding house situated in the former premises of the Conservatorio di Santa Maria Maddalena and attached to the teacher training secondary school, became part of the Regi Conservatori Riuniti.

In that same year, a convention between the institution and the Municipality of Siena was ratified, according to which the Municipality would rent part of the Refugio to dedicate it to the secondary school of Santa Caterina da Siena and its neighbouring kindergarten.
The collaboration with the municipality of Siena continued until 1964 with two interruptions. One in 1943, when the institution had to give shelter to refugees and evacuees, mainly from Livorno, and another in 1944, when the institution was offered to Italy's allies during the war. In 1964 the institution was gravely threatened when the building was condemned and the necessary architectural and administrative reforms were difficult to carry out. The then President of the administrative Commission, Professor Pietro Cinughi de Pazzi and his counsellors, Ingegner Giorgio Pini and Avvocato Giuseppe Angelotti, gave a fresh new start to the institution through an agreement with the University of Siena. This agreement meant that part of the institution was rented to the new faculties of liberal arts and philosophy, namely the rooms in Via Fieravecchia and the Palazzo di San Galgano, which were later bought by the University itself.

The agreement allowed the istitution to undertake the necessary reforms of the premises of Via del Refugio, which since 1976 have been dedicated to the insitution's boarding school, hosting young university students from all over Italy. The following memorandum of association includes the amendments to the former memorandum of 1955, which did not, however, alter the institution's historic mission of educating and preserving culture. The new rules had to be introduced to respect the provisions of article 1 from 3rd February 2006, n.27, which changed Conservatori Femminili Riuniti into a private organisation.