By the beginning of the War of the Second Coalition in 1799 he was an officer in the Cisalpine Republic acting as Aide de Camp (ADC) to Jean Victor Marie Moreau, then Barthélemy Catherine Joubert during the campaign in Northern Italy. After Joubert's death at the catastrophic Battle of Novi, Balabio fled with his troops and joined the forces under André Masséna, distinguishing himself as ADC during the siege of Genoa 1800, for which he was promoted Colonel.