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He arrived in Chile with Admiral Thomas Cochrane in November 1818, with the navy's ships intended to move the Army of the Andes to Peru.
During his period as an Officer in the Argentinian Army of the Andes protected his territory and liberated from the Spanish Crown, On 2 January 1817 the Buenos Aires city council appointed Estanislao Lynch as the major of Barracas.
In 1816 he joined the Army of the Andes, and returned to Chile as a battalion commander through the Planchón Pass (in southern Chile), occupying the city of Talca on February 11, 1817.
Bernardo O'Higgins and other Chilean leaders had fled to Mendoza during the new royalist government, which led to O'Higgins being part of the Army of the Andes as well as the Argentine soldiers.
He accompanied the latter to Peru, was promoted brigadier for his valor in the siege of Callao, and afterward as commander of cavalry engaged in the campaign of Peru, assisting in the battle of Junin, 6 August 1824, where he was dangerously wounded and saved from death by a Spanish soldier who formerly had served under him in the Army of the Andes.