Although Obando and Obaldía both belonged to the newly created Liberal party, they belonged to different ideological camps, Obando was of the Draconian faction (pragmatist but defenders of the death penalty), and Obaldía was of the Golgothian faction (radical liberal reformers) this brought them into conflict from the start as the Golgothians had opposed Obando's nomination in the first place.

In April 1854, Golgothians in congress moved to reduce the size and influence of the armed forces, thus provoking a coup by General José María Melo y Ortiz, commander of the Bogotá garrison.

Vice President Obaldía managed to escape by taking refuge in the US Legation in Bogotá headed by James S. Green, the United States Chargé d'Affaire to New Granada.

On 22 September, Congress convened in Ibagué, impeached President Obando for irresponsible negligence in not preventing the coup and formally removed him from office.

On 1 April 1855 Obaldía's term came to an end and Congress elected Conservative Congressman Manuel María Mallarino Ibargüen to succeed Obaldía as vice president and to finish Obando's term as acting president.