Forced out of business by the French invasion of 1796 he then entered military service as a commander of a detachment of cavalry, armed at his own expense with what remained of his fortune.

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.

In 1805, he commanded the 2nd Hussar Regiment (2.o reggimento Ussari Cisalpino) in the Kingdom of Italy and Guides as part of Domenico Pino's Division during the planned invasion of England in France.

Promoted brigadier general, he was appointed commander of the cavalry division under Pino in 1807 and moved to Pomerania to face the troops of King Gustav IV Adolf of Sweden.