During the final year of her school studies, Sr. Rani Maria felt an internal call to become the bride of Christ, the crucified. She shared her inner promptings with her cousin Sicily (Sr. Sony) who also thought alike. Responding to that personal call of Christ they decided to join the Franciscan Clarist Congregation.
Mary had anxieties about the reactions of her parents and relatives regarding her decision to join the convent. One day, she expressed her desire openly to her dear ones. Her brothers and sisters were not happy and asked their father not to allow her to go. The father replied: "but if she insists what shall I do? If God so desires, how can we go against it". The grandmother intervened: "Why do you oppose Marykunju joining the convent? Is she not going for a noble cause? How many parents desire that their children become priests and nuns? But does that happen? The vocation to the religious life is not given to all. God gives it only to some." Hearing these words of wisdom from the grandmother all remained silent. On 3 July 1972, Marykunju and her friend Sicily joined the convent at Kidangoor, near Angamaly.
Sr. Gladys, the mistress at the initial stage of her religious formation, says thus about Mary: “She always had a smiling face and was a smart girl. She did everything with perfection and had no complaints about anything. She did not need any corrections. Holding fast to what is true and just, she always spoke out things very openly." On 1 November 1972 Marykunju and 17 of her companions entered the next stage of formation called Postulancy and completed it in six months.
Mary was initiated in to the novitiate on 1 May 1973. During this period she formed herself to live a life based on the evangelical counsels. Sr. Infant Mary her Novice Mistress says about her novitiate days: "Mary was a faithful novice. She was quick to own up any mistake she would commit. I don't remember Mary taking an exemption from her studies, prayers, observance of the rules or work. She was always careful not to hurt anyone. At the same time, she was very charitable and showed sincere interest in correcting others. She always openly spoke out the truth."
The Lord uses cleansing measures to purify his beloved. In her life Mary too had her crosses to carry. Midway through her novitiate, she noticed that a black mark was growing on her leg. Even though she underwent some treatment, the doctors prescribed that she would not be healed completely. This caused her a lot of mental pain. All the same she was not desperate and went ahead believing and entrusting herself to the divine providence. The Lord rewarded her faith and cured her completely. In this manner the Lord prepared her interiorly for the religious vestition. Mary and the other novices made the First Profession and dawned the religious habit on 1 May 1974. The function took place in the St. George church; Angamaly officiated by the late Bishop Sebastian Mankuzhikary. On that auspicious day she received the name Sr. Rani Maria. She made her final commitment to the Lord by making Perpetual Vows on 22 May 1980. It was preceded by a preparatory course in Portiuncula, the generalate of the Franciscan Clarist Congregation in Aluva.