Flores was active in the Progaganda Movement and in 1894 traveled through the country with Faustino Villareal to spread the work and ideas of José Rizal.

Years earlier, he had become a Freemason because of his hatred of the abusive Spanish friars in the Philippine colony.

Flores was exposed to the work carried out by masonic lodges under the Gran Oriente de España, which are mainly composed of Spanish military men.

On September 8, 1898, Flores transferred the capital of Manila Province from Marikina to San Juan Del Monte.

As governor of Manila, he made divisions of municipalities and later turned them into battalions in preparation of the war against the Americans.

The victory of U.S. military forced Flores to go to Tarlac with the remnants of the revolutionary army and his family.

In April 1899, Flores, Col. Manuel Arguelles, and Col. Florentino Torres went to U.S. Gen. Arthur MacArthur to ask for cessation of hostilities.

[5] He saw that further resistance was futile and in 1900, along with several other generals and leaders, including Francisco Macabulos and Pantaleon Garcia, surrendered to the Gen. MacArthur in Nueva Ecija.

In December 1900, along with Florentino Torres, T. H. Pardo de Tavera, Cayetano Arellano, Felipe Buencamino, and Benito Legarda among others, Flores co-founded the Federalista Party.

After his governorship, he completed a law degree and passed his entrance exam for the Philippine Bar at the age of 62.