After France surrendered, he remained loyal to Philippe Pétain's new Vichy government, fighting aboard the Montcalm in the defence of Dakar against a Free French and British attack.

On 27 November 1942, when German forces broke into the naval port at Toulon, the Casabianca was "de relève" (i.e. with personnel and equipment available) rather than "en gardiennage d'armistice" (under armistice caretaking).

Jean L'Herminier chose to sail and break out for the open sea, but was unsure whether to obey his orders from admiral Darlan to scuttle in deep water or to join the Free French naval forces.

He discussed the matter with his officers and crew, who favoured the latter option, and so L'Herminier sailed for Algiers, under the control of British and American forces since Operation Torch, which had opened on 8 November that year.

He went to the US for medical treatment from August 1944 to July 1946, but still remained on extraordinary duties and represented the navy on the administrative committee of the Office national des anciens combattants (ONAC).