After the death of his mother he felt able to fulfil his long term plan of joining a religious community which would enable him to go to the foreign missions. In 1887 he went to Rome and became a member of the Catholic Teaching Society. In the novitiate he took the religious name Otto. The founder, Father Francis Jordan, soon entrusted him with the formation of the candidates. He also used his skills as a journalist for the benefit of the Society. In January 17, 1890 he was sent, together with the twenty-three year old Father Angelus Münzloher and Brothers Joseph Bachle and Marianus Schumm, to Assam in North East India where he became the first Superior. The work of this new mission was carried out with great zeal and energy. Father Otto wrote a catechism in the Khasi language, also a life of Jesus and Mary, and he had begun to translate the Bible. However, he fell ill with meningitis as a result of a heat stroke and died on 21st of August 1890.
Father Otto Hopfenmüller was a man with many talents and tremendous energy and it was a great encouragement to the newly formed Society when he joined. In his own words he says, ‘I have chosen to join the newly founded Catholic Teaching Society in Rome because it is in need of workers and because it has a good spirit, and in it I think I will be able to bear fruit for the Kingdom of God.’ It is certain that Father Jordan would not have been able to take on the responsibility for the mission in Assam without the knowledge that the leadership of the mission could be entrusted to Father Otto. Father Jordan knew he could rely on his energy, deep spirituality and extensive priestly experience. Although Father Otto Hopfenmüller died at the early age of thirty six years no one could doubt that he lived an accomplished and fulfilled Christian life.