In 1865 he was promoted to brigadier general and took command in the capital when President Pezet had to leave to face the advance of the revolution led in the south by Mariano Ignacio Prado and Pedro Diez Canseco. He tenaciously defended the Government Palace, which fell after a violent six-hour combat. Circumstances had made him face his own brother Pedro, who was inflexible, being arrested and removed from service. But then came the dictatorial government of Mariano Ignacio Prado, who, in 1867, after the victorious war against Spain, wanted to remain in power. This time, Francisco placed himself under the command of his brother, Pedro, who led the rebellion in defense of the Constitution from Arequipa, while he was conspiring in Lima. He received from his brother the appointment of political and military chief of the departments of the center, and had an important role in the fall of Prado, by taking Callao and then Lima, on January 8, 1868.