The Aagtekerke was deployed in the inter regional; between Batavia and Japan (Deshima) and in the Indonesian archipelago.

The Aagtekerke (Aechtekercke) was the fastest ship in a fleet of five VOC ships (De Tijger, Juffer, Luipaard & Bergen op Zoom) going from Batavia to Ternate with provisions and soldiers.

After having passed the Straits of Selayar, South Sulawesi. The Aagtekerke, the fastest in the fleet, went ahead to inspect an unidentified vessel sighted in the course of the fleet. In doing so the Aagtekerke ran far ahead. When the main body of the fleet had caught up, course was changed more to the South.

Aan hour before daybreak of March 4, 1650, the ships ran ‘gezamenlijck opt Riff vant eylandt Comboina’. (Coolhaas, 471)

All ships perished but crew and part of the cargo could be saved. The Aagtekerke was stuck but sound seated on the reef.

The remaining cargo was brought to Ternate by the Concordia yacht and the crew of the ships went to Batavia with a self-built ship from the wreckage, called 't Jagt van Vijven.

• Coolhaas, W. Ph. (1964).
  Generale missiven van gouverneurs-generaal en raden aan heren XVII der Verenigde Oostindische Compagnie.
  Martinus Nijhoff, 's-Gravenhage.
• NL-HaNA_1.04.02_1179B_0405.
• Liebner, H, et al (2016).
  Pra-Survey at Sagori Island, Southeast Sulawesi, Indonesia, the Scene of the Loss of a Dutch East India Company Fleet in 1650.