She entered Novitiate on 12th August, 1935. After one week of rigorous routine of Novitiate, Sr. Alphonsa developed a serious haemorrhage and a large ulcer on her leg which prevented her free movement. The superiors even thought of sending her back to Bharananganam. The bishop was consulted and after visiting her he decided that she should not be sent back. He preferred her death there, if it happens, rather than her being sent back.
Her condition remained crucial for a few months. At the suggestion of her Novice Master Rev. Fr. Louis CMI, a novena was started by the novices in common in honour of Bl. Kuriakose Elias Chavara. On the last day of the novena, Sr. Alphonsa had a vision of Bl. Kuriakose Elias Chavara who blessed her, touched her and said to her: “You are cured of this illness. And you won’t be affected by it again. But you will always have to bear up other sufferings.” Thus she was completely cured of her illness miraculously.
On completing her Canonical Novitiate, Sr. Alphonsa sealed her union with Jesus Christ by professing her Perpetual Vows to Him on 12th August, 1936. Sr. Alphonsa returned to Bharananganam and joyfully followed the Community life. But a few weeks later she had a severe attack of fever which lasted for six months. Tuberculosis was suspected. The whole community made novenas to Saint Little Flower and Bl. Kuriakose Elias Chavara. She was cured miraculously. When questioned insistently by the superiors, she confessed that a Carmelite nun came to her side, touched and healed her. She had a vision of Rev. Fr. Kuriakose Elias Chavara also.
Though Sr. Alphonsa got cured of the serious sickness, she was always tormented by minor ailments. The physical and mental agonies were unbearable, but she showed great patience, perseverance and fortitude. She wanted to become a saint at any cost. So she accepted and utilized suffering as a means of self-purification. “To suffer out of love and to rejoice in it, that is all that I desire on earth”- wrote Alphonsa in one of her letters. She considered everyone who had caused her any grief or suffering as ‘special divine instruments’ sent by God to sanctify her. She appeared quite well during daytime but suffered greatly at night. Those were sleepless nights for her. When asked ‘what she was doing during such time of the night?’ her response was that she loved. Having been miraculously healed Sr. Alphonsa got back to her regular life with others subjugating herself to all types of trials and hardships and emerging always victorious.
In spite of all her ordeals she loved God and her brethren. This was the secret of the success of her life. She enriched her life, living for others. She radiated the divine splendor around her with her cherubic smile that revealed the inner core of her spirit.
Further afflictions began to appear one by one. She became seriously ill due to an attack of fever. Doctor diagnosed it as double pneumonia. Careful nursing and prayer by the community brought her back to health. During this period a thief entered her room and she was seized with panic.
As a result of this encounter with the thief, she suffered a serious mental breakdown and started behaving like a child. She lost her memory and even the capacity to read or write. But even in this abnormal state of her mind, she was in deep communion with the Lord either praying earnestly for others or seeking pardon for the sins of others. It took almost one year to get back to the normal stage after the great shock.
No sooner had she recovered from her nervous breakdown than she was assailed with another affliction. There appeared a boil on her groin which slowly became an abscess causing unbearable pain. She was unable even to eat and her health deteriorated. Thinking that she has come to her last moments, the Last Rites were administered to her. But as foretold by Sr. Alphonsa, the crisis passed and on 30th September, the Death anniversary of St. Little Flower, she recouped her health.
Though Sr. Alphonsa had been a victim of suffering throughout her life, she never voiced any complaint. People enjoy the flowers and its fragrance, but nobody is bothered about the leaves at the bottom of these plants that decay to become the manure for its growth. St. Alphonsa was a mysterious saint who through her life of prayer and sufferings, wanted to be such leaves and lived like the leaf to decay and become the manure to produce flowers.
She appeared like a beautiful Rose where only the beautiful flower is visible to the onlookers. But it grows on branches with thorns which are unnoticed by others. She was always found with a serene smile even though the thorns of agony were hidden inside, since she knew that God Almighty wanted her to endure this excruciating agony to make in her a grandeur of virtues. She never regretted her sufferings. She even prayed for more sufferings and God was pleased to grant her lofty enthusiasm.
In July 1945 Sr. Alphonsa had an attack of spasmodic pain which threw her into fits of violent convulsions. It began with prolonged vomiting and her body became quite cold as if frozen to the marrow. This leads to complete exhaustion and helplessness which lasts for three to seven hours. She was seen bathed in perspiration and seemed to grapple with death. This type of violent convulsions occurred frequently till her death. She was ready to suffer anything for the love of Jesus Christ. She prayed to God to transfer to her the Malaria of Sr. Thresia and the Bishop so that it may not affect their busy and important schedule. God was pleased to grant the prayer of His beloved. Very soon the Bishop and Sr. Thresia were found to be completely cured and Sr. Alphonsa had contracted Malaria!!
The final phase of her agonies had persisted for over a year. She felt that it was time for her to join her beloved Spouse. She sought permission from Rev. Fr. Romulus and Mother Ursula to pray for her death. On 16th July, 1946 Sr. Alphonsa wrote to the Mother General Rev. Sr. Bernerditta like this: ‘Even as the kite snatches off the chicken, so will the Lord snatch me away’. On Sunday, 28th July, 1946 her saintly soul flew silently to her Divine Maker, without any one standing around her deathbed being aware of it.
The next day 29th July 1946, witnessed a funeral which was very simple. The coffin was carried in procession to the parish church by the sisters of the convent. At the Requiem Mass her special Spiritual Director gave the prophetic sermon. Her body was laid to rest in the tomb of the newly built cemetery chapel. It was providential that Alphonsa was buried at the very same spot where one finds her venerated tomb located today.