Burgos' nationalist views, codified in editorial essays, championing political and ecclesiastic reforms in favor of empowering more native clergymen, made him a target of opposition to civil authorities.

As a beholder to the evil treatment and apathy manifested by the Spanish clerical authorities to his comrades, Burgos felt oppressed.

To battle the injustice, he turned into a resolute and incredible backer for changes in the nation and a solid crusader for the rights and government assistance of the mainstream pastorate.

In 1864, an anonymous pamphlet was published in Manila, criticizing the prejudice in the Church, and providing rebuttals against several canards against the native clergy.

In 1869, Felipé Buencamino, a young student and an acquaintance of Burgos, was charged with spreading nationalist propaganda in the form of leaflets scattered throughout his school's campus, demanding academic freedom.

It was presided over by José María Basa, and included Agustín Mendoza, Máximo Paterno, and Ambrosio Rianzares Bautista.

[1]: 106 After the Cavite Mutiny on January 20, 1872, the trial of mutineer sergeant Bonifacio Octavo revealed that a man named Zaldua had been recruiting people for an uprising.

Nevertheless, governor-general Rafael Izquierdo reported to Madrid that the testimony had confirmed his suspicions, and pinned the blame on Burgos and two other priests, Jacinto Zamora and Mariano Gomez, for sedition.