[4] On arriving in Formosa, Junius took up residence in the village of Sakam, in the vicinity of Fort Provintia[5] 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.

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.