On his return to Batavia, he took up a post in the office of the bookkeeper-general (boekhouder-generaal), for whom he deputed for a long time, and whom he succeeded in 1657.

In 1659, he was placed in charge of the company's clerical and administrative staff (kapitein over de compagnie pennisten) in Batavia.

On 12 June 1663, Cornelis Speelman was appointed governor and director of Dutch Coromandel, but was suspended by the Heren XVII (Lords Seventeen), being accused of having illegally engaged in private trading.

Despite his strenuous protests, the court in Batavia wanted to make an example of him and he was sentenced to a 15 months suspension and a fine of 3,000 guilders.

He travelled once again, in 1669, as admiral of another expedition to Makassar where he completely subjugated the kingdom, receiving a gold chain and medallion in recognition of this the following year.

In December 1676, he led an expedition to Central Java, supporting the ruler of Mataram who was facing the Trunajaya rebellion.

He was called back to Batavia at the end of 1677 and on 18 January 1678 named First Counsellor and Director-General of the Indies (Eerste Raad en Directeur-Generaal van Indië).