A French garrison of a few hundred men took over the fort on 12 June. During the subsequent Maltese uprising and insurrection against the French, Maltese insurgents built Għargħar and Sqaq Cappara batteries to bombard Fort Manoel. The Maltese attacked the fort on a number of occasions, and the French retaliated with their own bombardment at least once. On 12 September 1799, a company of French troops from Fort Manoel attempted to silence an insurgent gun position in San Ġwann, but were repelled by the Maltese insurgents.