In May 1940, soon after the German invasion of the Netherlands, Werkman started a clandestine publishing house, "De Blauwe Schuit" ("The Blue Barge"), which ran to forty publications, all designed and illustrated by Werkman. Included there were a series of Hassidic stories from the legend of the Baal Shem Tov. On 13 March 1945, the Gestapo arrested Werkman, executing him by firing squad along with nine other prisoners in the forest near Bakkeveen on 10 April, three days before Groningen was liberated. Many of his paintings and prints, which the Gestapo had confiscated, were lost in the fire that broke out during the battle over the city.