Seventh child in a family of 13 children, Alphonsus joined the Jesuit noviciate of Sitagarha (Bihar) in 1957.

His Jesuit formation and training took him to Calcutta for a MA and doctorate in Indian philosophy (1963-1968) and to Austria (Innsbruck) and Germany (Tübingen) where he completed his Theological studies.

D'Souza served as bishop of the Roman Catholic Diocese of Raiganj, India from 1987 until his death in 2016.

At the time of his death (2016) the diocese counts 97300 Catholics, mostly underprivileged Santals belonging to the largest tribal group of India.

Having reached the age of 75 in 2014, and with failing health, Bp Alphonsus submitted his resignation to Pope Francis who requested him to remain in his post until a successor be found.