Tomás de Herrera also became acting President of the Republic of the New Granada for 3 months during the Colombian Civil War of 1854 against General José María Melo, who had committed a coup on 17 April.

In 1845, Herrera returned to national political life as governor of Panama and later minister of War and Navy of the government of José Hilario López.

Days later, Herrera managed to evade military custody by the regime that the Dictator José María Melo had established in Bogota.

Herrera continued his march and entered on April 23 in Tunja, thanks to the fact that Colonel Reyes Patria had defeated the National guard in the city.

Franco managed to build an army of 2,557 men with second commander General Marcelo Buitrago and chief of staff Colonel Jose Maria Rojas Pinzón.

Herrera left with his army from Tunja to Nemocón, a town where he arrived on May 19, and where he had to make one of two decisions: attack the column of Colonel Manuel Jiménez stationed in Zipaquirá, or continue the march to Honda to join to the forces commanded by General Joaquín París Ricaurte.

They departed with a battalion to join Joaquín París Ricaurte but did not succeed and subsequently sought to reach Ambalema by San Juan de Rioseco.

Herrera was finally able to get to Ibagué and install the executive branch, where he issued decrees which called on lawmakers to start meetings on July 20 in Bogota.

On July 15, Herrera rebuilt his cabinet, leaving Pastor Ospina in government, Jose Maria Soto Plata in Treasury, Ramon Mateus in Foreign Affairs and Pedro Alcantara Herran in War.

On December 4, 1854, after the attack deployed by the army on the southern side of the city of Bogotá, Herrera went into action in command of two battalions but he was seriously injured on the corner of the Pamplona and Bárbula avenues, and died shortly after.