Quesnel was placed on active duty with the Army of Italy on 6 February 1799. At the start of the War of the Second Coalition, Quesnel led a brigade in Paul Grenier's division. The division was made up of three battalions each of the 17th, 24th, and 106th Demi-Brigades, one battalion each of the 2nd Helvetica Legion and the 1st Polish Legion, 450 cavalry, and one foot artillery battery. He led his brigade at the Battle of Verona on 26 March 1799, the Battle of Magnano on 5 April, and the Battle of Cassano on 27–28 April. At the Battle of Bassignana on 12 May 1799, he was shot in the left forearm. At the Battle of Novi (1799) Quesnel led a brigade in Pierre Garnier de Laboissière's division. The brigade consisted of the 17th Light and 63rd Line Infantry Regiments. The painful arm wound finally compelled him to take a leave of absence from the army. Starting on 1 June 1801, Quesnel held a military post in the Cisalpine Republic. Two years later he took command of troops near Faenza.