After the creation of the "Grande Armée" in 1805, Frère was given a command and was cited several times in the bulletins, during the War of the Third Coalition. The next year, during the War of the Fourth Coalition, he was equally successful, being one of the first commanders to enter Lübeck, after the French led a successful battle against the Prussian defenders under Gebhard Leberecht von Blücher. On 5 June 1807, commanding a single infantry regiment, Frère forced no less than 10,000 Russians to surrender. He was promoted to General of Division in March 1808, before being sent to Spain, where he took the city of Segovia on 7 June 1808 and then served as chief of staff in the Army Corps of Marshal Jean Lannes during the bloody siege of Saragosa. He was created a Count of the Empire that year and in 1809 was recalled to the "Grande Armée d'Allemagne" in order to take part to the War of the Fifth Coalition against Austria, serving at the battles of Aspern-Essling and Wagram, where he received a serious wound during the second day of battle. In 1810, Frère was sent to serve in the "Army of Catalonia" and subsequently recalled to France and appointed at the command of the military division of Rennes. During the Hundred Days, Napoleon entrusted him with the command of the military division of Lille.