She was born as Annakkutty (little Anna) in Kudamaloor, a village in the princely state of Travancore which was under the British Raj (now present day Kottayam district, Kerala, India) to Joseph and Mary Muttathupadathu. She was baptized on 27 August 1910 at Saint Mary's Church in Kudamaloor under the patronage of Saint Anna. Anna's mother died when she was young, so her maternal aunt raised her. Anna was

In 1916 Anna started her schooling in Arpookara. She received First Communion on 27 November 1917. In 1918 she was transferred to the school in Muttuchira. In 1923 Anna was badly burned on her feet when she fell into a pit of burning chaff. This accident left her permanently disabled.

When it became possible, Anna joined the Franciscan Clarist Congregation. She arrived at the Poor Clares convent at Bharananganam on Pentecost 1927. She received the postulant's veil on 2 August 1928 and took the name Alphonsa. In May 1929 she entered the Malayalam High School at Vazhappally. Her foster mother died in 1930.

On 19 May 1930 she received her religious habit at Bharananganam. Three days later she resumed her studies at Changanacherry, while working as a temporary teacher at the school at Vakakkad. On 11 August 1931 she joined the novitiate. Anna took her permanent vows on 12 August 1936. Two days later she returned to Bharananganam from Changanacherry.