On arriving in Formosa, Junius took up residence in the village of Sakam, in the vicinity of Fort Provintia in present-day Tainan City. Described as more energetic than his contemporary, George Candidius, Junius was involved in the pacification of Taiwanese aborigines following the slaughter of sixty Dutch people by the natives of Mattau. This took the form of a short punitive war against the offending villages by Dutch forces, resulting in the killing of "a few dozen" aborigines and a Pax Hollandica which followed after the recalcitrant tribes had been cowed. Following this campaign, Junius continually urged the authorities in Batavia to send more clergymen to Formosa to assist in the instruction and conversion of the now amenable natives, something in which he was supported by the governor of the time, Hans Putmans. However, he was ultimately disappointed by the response from the colonial administrative centre. In 1636, Junius established the first school in Formosa, teaching a class of 70 boys to write their mother tongue in roman letters. In 1641, he was called to Batavia to report to the Consistory, and asked whether he would like to continue his service in Formosa. He agreed to return for two years, provided that These requests were agreed upon, and Junius returned to Formosa until late 1643. The numbers of baptisms under Junius' authority were impressive, even with Junius' work confined to the few villages around the Dutch strongholds of Fort Zeelandia and Fort Provintia. One commentator remarks that
On December 14, 1643, Junius again went to Batavia at the end of his commission. The Consistory again requested him to return to Formosa to continue his ministry, but this time Junius declined and decided instead to go back to his homeland, Holland. He married in 1645 in Delft, lived on Koornmarkt until 1653 when he accepted a post in Amsterdam. He died of the plague in Amsterdam in 1655.
The American Antiquarian Society holds the following volume: Of the conversion of five thousand and nine hundred East-Indians, in the Isle Formosa, neere China, to the profession of the true God, in Jesus Christ; by meanes of M. Ro: Junius, a minister lately in Delft in Holland; Related by his good friend, M. C. Sibellius, Pastor in Deventer there, in a Latine letter; translated to further the faith and joy of many here, by H. Jessei, a servant of Jesus Christ by the author Caspar Sibelius.
