The formation of East Timorese Jesuits follows the universal formation process of the Society of Jesus: Novitiate, Juniorate, Philosophy, Regency, Theology, and finally, Tertianship. It is at the end of Theology studies that a Jesuit scholastic is ordained a priest. In the case of a Jesuit Brother, a formation program is designed to suit the capacity of the Jesuit and the need of the Region or the Province to which the Jesuit Brother belongs.

Although the Society of Jesus began to accept local Timorese men in the late 1970s, it was not until 2002 that a Candidacy Program was introduced to recruit and prepare young men to enter the Novitiate.  The Casa Gonzaga Jesuit Candidacy accepts young men who desire to discern their vocation to the Society of Jesus. In 2008, the Manresa Novitiate opened in Lahane, Dili. Prior to this, Novitiate formation was done in Indonesia and Singapore. From 2016, candidates are enrolled in two-year or four-year courses in the Instituto São João de Brito.

After two years of Novitiate formation, a novice professes his first and perpetual vows in the Society of Jesus. He then becomes a scholastic and begins formal studies in the Juniorate Program. Since 2014, the Timorese Juniors join other Jesuit Juniors in Sri Lanka for a year of English language studies and preparation for tertiary studies. After a year, the Junior proceeds to do his studies in Philosophy. Many Timorese scholastics go to Loyola College in Chennai, India, for this.

The formation of a Jesuit does not, however, end with his ordination to the priesthood. After a few years of pastoral work, preferably in his own country, the Jesuit is invited by his Superior to enter the final stage of formation called Tertianship.  It is only upon completion of this final stage of the formation that he is invited for full and total incorporation to the Society of Jesus.