It is known that Núñez participated as a 15 year old in the War of the Supremes (1840), the first of many Colombian civil wars, which was caused by the military uprising of a number of political leaders (the "Supremes") in the provinces in the South of the country against the centralist and conservative government of José Ignacio de Márquez. Núñez joined the revolutionary side and participated in the siege to his own hometown, Cartagena. Following the war, he entered college and obtained a degree in Law from the Universidad del Magdalena e Istmo in 1844. By 1848 Núñez had founded in Cartagena, Colombia, the newspaper "La Democracia", with the intention of promoting the presidential election of General José María Obando, the leader of the insurrection in the War of the Supremes, as a successor to José Hilario López. The same year, Obando had been elected as governor of the Province of Cartagena and he appointed Núñez as Chief of Staff in Cartagena's government, thus beginning his political life. He would maintain the position until 1853, with Obando as president, when he decided to move to Bogotá to become a member of the Colombian Congress, and where he made a name for himself by fighting the federalist and socialist ideas of Manuel Murillo Toro. Following the coup against Obando in 1854 by José María Melo, Núñez went into hiding, but then was elected as governor of the department of Bolívar, which contributed to the defeat of Melo. The newly appointed president Manuel María Mallarino made Núñez, minister (secretary) of War in 1855, and then Minister of the Treasury. His excellent results as Minister of Treasury would bring him wide recognition. In 1855, he also published his first volume of political essays, under the name of "La Federación".