On his return to Chile in 1802, a contrary wind landed him in La Guaira, from where he traveled to Caracas where he obtained a canonry in the cathedral in 1803.
He took part in the patriotic movement, and when on 19 April 1810, in the meeting of the municipality, the captain general, Vicente Emparan, was about to be victorious, Cortés de Madariaga was sent for and took a seat in the assembly as deputy of the clergy.
He was sent in 1811 as a commissioner to the patriots of New Granada, but in 1812 was included in the capitulation of Miranda, and sent by Monteverde as a prisoner to Spain, where he was confined in the penitentiary of Ceuta.
But the other chiefs of the eastern provinces did not recognize the authority of this congress or the governing junta, and before the approach of the enemy Cortés de Madariaga fled to Jamaica.
In 1820 Cortés de Madariaga joined the expedition of General Montilla against Riohacha and Santa Marta, and fixed his residence there, while Caracas, which had become his second home, was occupied by the Spaniards.