For the first time Fermin Palacios headed the country in 1844, for seven days (from February 1 to February 7). It was a period in which a fierce struggle was waged between those who supported General Francisco Malespin and those who supported the Bishop of San Salvador Jorge de Viteri y Ondo in the Legislative Assembly for the presidency; Palacios turned out to be a convenient temporary figure that suited both sides. In the end, supporters of Malespin won.
On February 15, 1845, Vice President Joachim Eufrasio Guzman declared the absent President Malespin deposed; at the time of the new presidential elections, Fermin Palacios was again appointed at the head of the country. April 25, Gusman took office as president of the country.
Guzman stood for free presidential elections, and for the time they were held, on February 1, 1846, he again transferred his presidency to Fermin Palacios. On February 21, Eugenio Aguilar was elected the new president of the country. It was a difficult period in the history of the country, and on July 12 Aguilar transferred the presidency to Palacios, but on July 21 he returned it to himself.