In 1812, he refused to swear allegiance to the Provisional Constitution of 1812 [es], and in response he was declared guilty of treason against the state and relegated to Colina.

Though assuming the ecclesiastical authority of the diocese of Santiago in 1816, he had only four years of actual governance of it (out of the 17 of his official term), since when not confined somewhere within Chile, he was exiled from the country.

[1] This suspicion was brought about by the recent opposition of the papacy to the independence of the countries of Latin America, as had been highlighted in the encyclical Etsi longissimo terrarum [es], which called for "uprooting and completely destroying the baleful weeds of riot and insurrection that the enemy sowed in those countries" of "America, subject of the Catholic King of Spain".

[2] Amid the ensuing controversy between Rodríguez Zorrilla, the independent canon José Ignacio Cienfuegos, and the government, the bishop was shipped to Acapulco, which he left (via Veracruz, New York, and Le Havre) for Madrid.

...Note that the ideas of our ancestors, founders of the Republic (of Chile), were such with regard to the Roman curia that once Mariano Egaña – there was no better Catholic – had written that the bishop Rodriguez was corresponding with Rome, they put him on a mattress at midnight and sent him to Mexico.José Santiago Rodríguez Zorrilla died in Madrid in 1832.