The Congregation of the Franciscan Sisters of the Immaculate Heart of Mary traces its beginnings to Pondicherry on 16 October 1844. It holds the distinction of being the very first indigenous religious institute for women in the whole of Asia. Rev. Fr. Louis Savinien Dupuis, MEP, a French missionary, founded this congregation in response to a significant need identified by the Fathers of the Diocesan Synod of Pondicherry: the upliftment and education of women.

During the Synod, Msgr. Clement Bonnard, the Vicar Apostolic of Pondicherry and President of the gathering, strongly emphasized the vital role of women's education in shaping virtuous families and raising overall social and spiritual standards. The Synod Fathers envisioned the formation of an Indian women's congregation that would take up the mission of educating women—imparting not only academic knowledge, but also religious and moral instruction.

With the blessing of Pope Gregory XVI and the approval of Msgr. Clement Bonnand, the foundation for this new congregation was laid. On 23 February 1859, it was affiliated with the Third Order of St. Francis, and in 1864, Msgr. Godelle formally recognized it as a diocesan congregation. Later, on 18 July 1886, it was officially united with the Third Order of St. Francis. Under the dedicated leadership of Fr. Dupuis, the congregation steadily grew and expanded into neighboring dioceses. He remained deeply committed to its development until his death on 4 June 1874, after which he was buried in the Cathedral. His remains were later exhumed and ceremonially reinterred on 13 April 1989 at Nirmala Novitiate, Pakkumudayanpet, Pondicherry.

Following the Founder's death, Sr. Maria Natchatram—one of the first four sisters to join the congregation—became the first Superior General. A council of four members was instituted under the direction of Rev. Fr. Francis Berges. With the support of successive Directors, many of whom were priests of the Paris Foreign Missions, the congregation flourished and spread widely, much like the biblical mustard seed.

In 1946, after consultations with the bishops of Pondicherry, Kollam, and Vijayapuram, and with the General Council, the Holy See authorized the Apostolic Delegate of the East Indies to separate the Malayalam-speaking members from the main body of the congregation. This division was carried out in 1947, giving the sisters from Kerala the choice to remain with the Tamil section or join the Malayalam section. Those who opted for the Malayalam group went on to form a new congregation: the Congregation of the Immaculate Heart of Mary, Quilon.