Camphuys survived the disaster and left on 23 August 1653 aboard the Golded Dragon.

After a year, as usual for that position, he returned and held the function another 2 times (in 1673 and 1675) alternated with the membership of the Council of Justice.

On 11 January 1684 Joannes Camphuys was appointed by the Council of the Dutch East Indies as successor to Cornelis Speelman as Governor-General, initially as provisional Governor-General until the Lord XVII approved the appointment.

Because a number of people felt passable in the appointment, his understanding with the council was not optimal.

Noteworthy are the Soerapati uprising on Java and the tract with Bantam of 17 April 1684.

However, he had a lot of interest in science and he supported them wherever possible and also wrote a dissertation on the foundation of Batavia included in François Valentine's standard work, Old and New East Indies.

Camphuys was three times sent to Japan as Opperhoofd or chief negotiant and officer of the VOC trading post.