Schérer served as French Minister of War from 22 July 1797 to 21 February 1799. When the War of the Second Coalition broke out, Schérer was given command of the Army of Italy once again. He won an initial clash at Pastrengo on 26 March. But he proved unable to stop the Russo-Austrian advance. He was defeated by Austrian General Pál Kray at the Battle of Magnano on 5 April. "Schérer went into this battle without forming a reserve and was thus unable to react to crisis or opportunities effectively." Forced to retire behind the river Mincio, he gave up command to Jean Moreau. Because of his loss of Italy he was forced to appear before a committee of inquiry. After securing an acquittal, he retired to private life on his estate at Chauny in Picardy, where he died in 1804.