In January 1939, Moulin was appointed préfect of the Eure-et-Loir département. After war against Germany was declared, he asked multiple times to be demoted because “his place is not at the rear, at the head of a rural departement”. Against the opinion of the Minister of the Interior, he asked to be transferred to the military school of Issy-Les-Moulineaux, near Paris. The Minister forced him to return to Chartres, where he had trouble ensuring the safety of the population. When the Germans got close to Chartres, he wrote to his parents, “If the Germans — who are able to do anything — make me say dishonorable words, you already know, it is not the truth”.
He was arrested by the Germans on June 17th, 1940, as he refused to sign a false declaration that three Senegalese Tirailleurs had committed atrocities, killing civilians in La Taye ; in fact those civilians had been killed by German bombings. Beaten and imprisoned because he refused to comply, Moulin attempted suicide by cutting his throat with a piece of broken glass. This left him with a scar he would often hide with a scarf—the image of Jean Moulin remembered today. He was found by a guard and taken to hospital for treatment.
Because he was a Radical, he was dismissed by the Vichy regime of Marshal Petain on November 2, 1940 , along with all other left-wing préfets. He then began writing his diary, First Battle, in which he relates his resistance against the Nazis in Chartres; this was later published at the Liberation and prefaced by General de Gaulle.