She remained in the area for a couple of days and was then ordered to bombard the Dutch aerodrome at Waalhaven in Rotterdam, which had been occupied by German paratroopers.

She arrived in Hook of Holland, but after the loss of the destroyer Van Galen during her attempt to do the same, the operation—of which Flores was also part—was cancelled.

As part of the Battle of the Afsluitdijk, Johan Maurits van Nassau was ordered by Den Helder on 12 May 1940 to silence a German battery near the Afsluitdijk, and on 14 May, she bombarded the German battery (consisting of 88 mm (3.46 in) guns of the 1.

There was a general evacuation of personnel and ships, and Johan Maurits van Nassau left Den Helder on 14 May with the minelayers HNLMS Jan van Brakel, Douwe Aukes and Nautilus, and the torpedo boats G 13 and G 15.

Johan Maurits van Nassau received two or three hits, one of which caused a fire near an ammunition stack.