Born as Annakkutty in Kudamaloor, a rural village in Kottayam district, Kerala, India, to Joseph and Mary Muttathupadathu. She was baptized on August 27, 1910 at Saint Mary's Church in Kudamaloor under the patronage of Saint Anna.  Anna's mother died when she was very young, so her maternal aunt raised her. Anna was educated by her great-uncle Father Joseph Muttathupadathu. When Anna was 3 years old, she contracted eczema and suffered from it for over a year.

In 1916 she started school in Arpookara. She received First Communion on November 27, 1917. In 1918 she transferred to the school in Muttuchira. In 1923 Anna badly burned her feet when she fell into a pit of burning chaff. This accident left her permanently disabled. She arrived at the Poor Clares convent at Bharananganam on Pentecost 1927. She received the postulant's veil on August 2, 1928 and took the name Alphonsa. In May 1929 she entered the Malayalam High School at Vazhappally. Her foster-mother died in 1930.

On May 19, 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 August 11, 1931 she joined the novitiate. She took her permanent vows on August 12, 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 she was reportedly cured from her ailments through the intervention of Saint Thérèse of Lisieux and Blessed Kuriakose Elias Chavara, but on June 14, 1939 she was struck by a severe attack of double-pneumonia, which left her weakened. On October 18, 1940, a thief stumbled into 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 September 29, 1941. The next day 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 July 28, 1946, aged 35. She is buried at Bharananganam, South India in the Diocese of Palai.