The Franciscan Ashram at Nattakkal in Kasargod District, Kerala in the eparchy of Tellicherry began on November 22, 1993 with the arrival of Fr. Manuel Manicompel who stayed in the house on the twenty-one acres and sixty two cents of land purchased by the Mission. The Canonical erection was on September 17, 1994. Fr. Manuel was appointed the first Superior.

On November 8, 1993, Bishop Mar George Valiyamattam of Tellicherry blessed the foundation stone for the future Church of St. Francis of Assisi that was laid by Fr. Alfred Calleja, Minister Provincial of Malta. The same Bishop did the blessing and consecration of the Church on September 17, 1994.
Fr. Alfred Calleja, Minister Provincial of Malta on February 2, 1995 during the celebrations to mark the establishment of the Provincial Custody, blessed the newly constructed Ashram.

The Pre-Novitiate was transferred to Franciscan Ashram from Kolbe Ashram on August 15, 1995. Fr. Mario Franchi, Minister Provincial of Tuscany, Italy, blessed the new Pre-Novitiate building on January 9, 1996. In 2005 the Pre-Novitiate was transferred to Padua Franciscan Ashram, Puthenchira and from May 2006 to May 2008 it served as the residence of one group of Orientation year students.

The Church, the Friary and the Pre-Novitiate are constructed on the plans of Fr. J.M.Stevens S.J. of Bangalore.
On January 1, 2003 the Ashram Church was declared a parish and Fr. Manuel Manicompel was appointed the first parish priest.
The newly constructed Cemetery of the parish near the Ashram Church was blessed by Fr. Joseph Cilia, Provincial Custos on July 3, 2004.