In summer 1337, with the outbreak of the Hundred Years War, he provided a contingent of 6,000 men for the campaign of Raoul I of Eu, Constable of France, in Gascony.

In July 1338, he attended a general conference at La Réole, but before achieving anything of note, John and his fellow captain-general in the south, Gaston II, Count of Foix, were called north to help counter the expected invasion of Northern France by King Edward III of England.

As this threat grew weaker the French offensive in the south was resumed with the siege of Penne-d'Agenais in November by John of Bohemia and the Count of Foix.

Through these early years of the war the Gaston II, Count of Foix had conducted a series of independent campaigns which allowed him to expand his personal territory into the Adour valley and the Landes.

Just after his return from the north at the end of 1339 John attacked Miramont-Sensacq, a small town he laid claim to, but which was situated in territory dominated by the Count of Foix.

As compensation for the territory he expected to lose once he switched allegiance Armagnac demanded several towns held by the King of France, chief among them Montréal, Mézin and Condom.

On 26 July what begun as an unauthorized attack on the enemy lines by some French knights developed into a major battle as the Duke of Burgundy decided to sally forth in strength.

During the Battle of Saint-Omer the Count of Armagnac with his retinue of 300 heavy cavalry succeeded in breaking the Flemish left and then in the following pursuit causing several thousand casualties.

In August 1345 Armagnac was laying siege to the Anglo-Gascon garrison at Monchamp outside Condom when Henry of Gosmont, Earl of Lancaster arrived in Bordeaux.

In September 1346, following the French defeat at the Battle of Crécy and the beginning of the English Siege of Calais, Armagnac was appointed royal lieutenant in the south-west.