Isabella of France, queen consort of England, and her son (later Edward III of England) embarked from Crotoy for Holland and then England in 1326, in order to overthrow their husband and father, Edward II. During the Hundred Years' War the town was alternately under English and French control. Edward III stayed in Crotoy and in 1340 built a very important fortress. Besieged by the English, Crotoy, the last French position in the Bay of the Somme, surrendered on March 1, 1424. After the Battle of Verneuil, Jean II, Duke of Alençon was interned there for three years. Joan of Arc was imprisoned there before being taken to Rouen for trial. During these troubled times, Crotoy was the place of residence of a governor and a garrison. Jacques d'Harcourt was the most famous governor: he defended Crotoy boldly and courageously against the Anglo-Burgundian armies. An eponymous street pays homage to him in the city center.
During the wars of religion, Crotoy took the side of Henri de Navarre. By an edict of 1594, Henri IV relieved the Crotellois from taxes. He stayed in the town on April 18, 1596.
In 1674, under the terms of the Treaty of Aix-la-Chapelle, the castle of Crotoy was destroyed.