The encounter between the Jesuit missionaries and the St. Thomas Christians or Syrian Christians in Kerala in the second part of the sixteenth century was for both sides a significant opening to different cultural beliefs and routines. An important and understudied outcome of this encounter, documented here on the Jesuit side, was the possibility of accepting religious plurality, at least within Christianity. The answers to the questions of how to deal with religious diversity in Christianity and globally, oscillated between demands for violent annihilation of the opponents and cultural relativism. The principal argument in this paper is that it was the encounter with these "ancient" Indian Christians that made the missionaries aware of the importance of the accommodationist method of conversion. This controversial method, employed in the Jesuit overseas missions among the "heathens", was therefore first thought out and tested in their mission among the St. Thomas Christians in the late sixteenth century.