When the war broke out, she was in the West Indies awaiting the arrival of the new gunnery training ship Van Kinsbergen, which would relieve her of her duties there, allowing the Maurits to return to the Netherlands. On 10 May 1940, she was stationed as a search and guard vessel at Vlissingen. She immediately became a target of German planes, of which she managed to shoot down one. After remaining in the area for a couple of days, she was assigned to bombard the Dutch aerodrome Waalhaven, which was occupied by German paratroopers. She arrvied in Hoek van Holland, but after the tragic loss of the Van Galen during her attempt to do the same, the operation ( of which the Flores was also part ) was blown off. She was ordered to Den Helder on May 12 1940, with the intent to use her to silent a German battery near the Afsluitdijk. She fired a few shots to see if the range was not too big. These shots proved it could be done, and on 14 May, she bombarded the German battery ( 88 mm'ers of the 1st Cavalry Division ) and silencing her from over 18 kilometres away. On the way back, she was fiercely attacked by German planes, but she remained undamaged, to great surprise of all. The struggle on Dutch soil was however coming to an end, and the role of the Navy had ended. A general evacuation of personell and ships was ordered, and the Johan Maurits van Nassau (Luitenant 1e Klasse Pieter Kronenberg) left Den Helder on May 14 along with the minelayers Jan van Brakel, Douwe Aukes and Nautilus and the torpedoboats G 13 and G 15. In the afternoon, they came under attack of several German planes, about 10 miles west of Callantsoog. Especially the Maurits, being the largest vessel of the convoy was the target, and she received two or three hits, one of which caused a fire near an ammo stack. Abandon ship was ordered, and most of the crew managed to leave the ship. Eight crewmen were killed during the attack or abandoning ship. Later, most of those crewmembers were transported back to Den Helder by the rescue vessel Dorus Rijkers, but some were lucky enough to remain aboard the ships going to England.
The wreck lies in 20 meters of water about 5 nautical miles west of Callantsoog, Netherlands in position 52º50'13"N, 04º33'56"E.