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 Clare’s 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.
She taught elementary school, but was often sick and unable to teach.
In December 1936, it is claimed that she was cured from her ailments through the intervention of Blessed Kuriakose Elias Chavara, but on 14 June 1939 she was struck by a severe attack of pneumonia, which left her weakened. On 18 October 1940, a thief entered her room in the middle of the night. This traumatic event caused her to suffer amnesia and weakened her again.
Her health continued to deteriorate over a period of months. She received extreme unction on 29 September 1941. The next day it is believed that she regained her memory, though not complete health. Her health improved over the next few years, until in July 1945 she developed a stomach problem that caused vomiting.
She died on 28 July 1946, aged 35. She is buried at Bharananganam, Travancore (present day Kerala) in the Diocese of Palai.
Her tomb in Bharananganam has become a pilgrimage site as miracles have been reported by some faithful. The miracle attributed to her intercession and approved by the Vatican for the canonization was the healing of the club foot of an infant in 1999.