Jan Pieterszoon Coen left Batavia for the last time on 28 June 1939 and was stationed in Amsterdam on 29 July 1939 where she was waiting to be scrapped.
When the German Army invaded the Netherlands in May 1940, the Royal Netherlands Navy made a plan which involved scuttling Jan Pieterszoon Coen at the entrance of the port of IJmuiden in order to prevent German warships entering the harbor.