The Congregation was started at Changanacherry on December 14, 1888. It took its origin from a fraternity of Franciscan tertiaries of the parish of Palai. A small group of eight pious ladies was leading a community life at kannadiurumbu, Palai. Rt. Rev. Dr. Charles Lavingne, the then Vicar Apostolic of Kottayam, happened to visit this community on July 4, 1888. The pious ladies expressedtheir desire for a fuller Franciscan life. He felt that it was not an easy task. Yet His paternal solicitude resulted in founding a new offshoot of the Franciscan family in Kerala on December 14, 1888: The Franciscan Clarist Congregation..

The Infant Congregation soon flourished within and outside the Diocese of Changanacherry. In twenty Provinces and four Regions, there are 695 Houses and 6750 members excluding novices and postulants. St. Alphonsa is a member of this congregation. Sr. Rani Maria, a martyr for truth and justice, is also a member of the Congregation

His Holiness Pope Pius XII bifurcated the Diocese of Changanacherry and created the diocese of Palai on July 25, 1950. As a result the Franciscan Clarist Congregation also was divided into two independent units: Changanacherry and Palai. Palai unit was again divided into two Provinces: Alphonsa Province, Palai and Alphonsa Jyothi Province, Bharanganam.

In 1951 Rev. Fr. John Thottuvely, vicar, Ss. Gervasis and Prothasis Church, Kothanalloor and the parishioners made a request to Rev. Mother Ursula, Superior, Clarist Convent, Bharananganam, to open a branch of the Congregation at Kothanalloor and she was in favour of the request. On June 3, 1951 six Rev. Sisters came over to Kothanalloor from Bharananganam. Shri Mathew Pallikaparampil (Thadathil) was good enough to allow the sisters to stay in a building of hisown at Mudappa. On August 11, 1956, the Rev. Sisters shifted their residence to the present quarters near to the church. The new branch of the Congregation is named “Fatima Matha Franciscan Clarist Convent.” The then Vicar Rev. Fr. Alexander Neerackal and the parishioners could help the convent a lot.

The Rev. Sisters are involved in education and social works of the parish. The community adopted two orphan girls in 1969. One of them is a religious sister working in North India. The other one leads family life.

In 1990 the sister started Alphonsa Balikabhavan intended to be maintained for the reception, care, protection and welfare of children (Girls). Yearly they give admission to 25 poor girls. More than two hundred girls have gone out of this Bhalikabhavan after SSLC exam.

Infant Jesus English Medium Nursery is under the management of the convent. At present there are 14 sisters in this convent.