With the information that the British fleet was about to invade, the viceroy sent most of his troops to Montevideo, as it was thought to be the central focus of the invasion.

Ruiz Huidobro organized an expedition to recapture Buenos Aires, but just as he was ready to leave, captain Liniers arrived with fresh information about the local resistance that was being formed, and he was given command of the troops.

About the same time, the cabildo in Buenos Aires decided on the ouster of viceroy Sobremonte and his replacement by the second in command, Ruiz Huidobro.

During the revolution of 1 January 1809, after the failure of the first attempts by Martín de Álzaga, he supported Bishop Lué's idea of replacing Liniers with the most senior officer.

Following him at the Cabildo, Saavedra spoke supporting his argument but proposed instead a new form of government by a Junta, the motion that won the day.

He was not tried, but found it more prudent to travel to Chile, where he planned to offer his military services and experience to the dictator José Miguel Carrera.