During World War II, he served as Resident-General in Morocco and Commander-in-Chief in French North Africa. Noguès was appalled by news that the French government was seeking an armistice with Germany. On 17 June 1940 he telegraphed to Bordeaux, where the government was then situated: "The whole of North Africa is appalled. The troops beg to continue the struggle if the government has no objection. I am ready to take responsibility for this attitude with all the risks that it entails," i.e. asking for a hint to carry on fighting. However, he did not approve of General Charles de Gaulle's call from London on 18 June to carry on fighting, telling the British liaison officer that he thought de Gaulle's attitude "unseemly" and forbidding the North African press from publishing de Gaulle's appeal.