Henriques took the wish of Xavier seriously and learnt Tamil so well that he could converse with Tamils fluently, hear their confessions. and explain to them effectively the Catholic belief system. When in 1549 Criminali was killed at Vedalai by soldiers of the raja of Ramnad, Jesuits in the Fishery Coast elected Henriques as the new Superior of the mission, which was later approved by Xavier. The three reasons given by the Jesuits for their choice of Henriques as their mission Superior was that he was the apt person for the job, he understood the language of the local people, and he had a good relationship with the local people (Wicki 1963).

Henriques insisted that the Jesuits coming to the Fishery Coast should learn first of all the language of the people before anything else. The importance given to language was such that the Jesuits decided to speak among themselves only in Tamil. If they failed to speak in Tamil, they took upon themselves some penance or other.

When Henriques was Superior of the mission, new institutions were established in quick succession. An elementary school already existed in Punnaikayal. To that, a higher grade school was added. Thus promising young men were given the opportunity to receive further studies there so that they could gain enough knowledge to be able to complete their studies in the college in Kollam, Kerala, directed by Fr. N. Lancilotti. The aim of this type of education was to create well-brought-up and influential Christians, who could, by their example and superior knowledge, show others a truly Christian spirit and turn of mind (Castets 1926).

From 1549 onward Henriques selected a group of men from among the Christians in the Fishery Coast who were best instructed in the Christian faith and lived an exemplary life for a special mission. When they expressed their willingness to spend their lives spreading and witnessing the message of Jesus without receiving any salary, he invited them to make a public act of oblation and offer themselves to God. Henriques had a high regard for the quality of the Christian life of these itinerant preachers. He called them “these brothers of ours” and wrote high praise of them in his letters. For example, on January 12, 1551, he wrote from Kochi to his companion Simon Rodrigues in Portugal:

They itinerant preachers in the Fishery Coast] show a great desire to serve God and they do this every time in a better way. They are quite ready to obey the Fathers, as if they lived under obedience, and they are quite ready to die for the love of Christ Our Lord. You may believe that one of the great consolations which we, Fathers and Brothers, have here is to see these men, or better these brothers of ours, because we consider them as such for their great virtue and for the deep friendship they have with us. And it is certain that in some of them we notice such virtues that we would be very grateful to God our Lord if he would grant them to us. Such men edify the people very much by their good life, free from all self-seeking. And so, after they are placed in the various villages, by the goodness of God a very different fruit is produced in those places compared with the earlier times [when only foreign missionaries worked there]. (Wicki 1950, 155)

In 1560 Henriques organized devout men and women of the coast into a confraternity of charity. Confraternity was one of the ways adopted by the Jesuits worldwide to seek lay collaboration in their ministries to the people. It was almost like a religious society for married people. Its members were expected to lead devout Christian lives and do works of charity, like the Jesuits, by helping those in need—the sick, poor, and abandoned. They established small hospitals in some villages and took care of the sick and dying. In Punnaikayal, Tamil Nadu, Henriques founded a hospital where the sick and invalids could be properly taken care of. Manual Coutinho, the Portuguese captain, fully supported this venture. A local Catholic couple managed the running of the hospital.

By 1600 twenty Jesuits (17 priests, 2 coadjutor brothers, and 1 scholastic) were working in the Fishery Coast. There was a desire among the Jesuits to move into newer areas and establish Christian communities there.