The viceroy Antonio José Amar y Borbón initially presided over the junta in Bogotá, but due to popular pressure, he was deposed five days later.
[3] These juntas made a case over their legality and legitimacy within the monarchy, and declared loyalty to Ferdinand VII, to the Catholic church, and to maintain ties with Spain.
Just as the local councils were fundamental in the attainment of a peaceful transfer of power, particularly in the large cities, they soon became a source of strife and territorial disintegration following the ousting of the regal authorities.
Royalist factions commanded by Spanish officers managed to seize power in the cities of Santa Marta, Panamá (by then, still a part of the vice-royalty of New Granada), Popayán and Pasto, and soon engaged in conflict against the regions with autonomous governments.
While the royalist regions were military weak and were often defeated by the juntas, they managed to become a source of destabilization which both maintained the idea of reconciliation with Spain alive, and drained the resources and energy of the patriotic governments.
[2] The Supreme Junta of Santafé (in modern-day Bogotá) assumed that it would inherit the authority of the old regime, as it was the most prosperous and populated province in the vice-royalty, and it was in fact the seat of the Spanish viceroyalty.
Following a failed royalist coup d'état, Cartagena became the first province in New Granada to formally declare its independence from Spain on November 11, 1811 (the day is also today a national holiday in Colombia).
The act, however, failed to integrate New Granada as a whole entity, particularly due to the energetic opposition of Cundinamarca, and only made the differences between centralist and federalist ideas even stronger.
Nariño and his followers became ardent opponents to federalism and to the congress, and were convinced that the economic and political power of Cundinamarca would allow it to dominate and unify New Granada.
Nariño convened an assembly to revise the constitution of the state and make it even more centralist, and then decided to annex the surrounding provinces of Tunja, Socorro, Pamplona, Mariquita, and Neiva, but was mostly unsuccessful on both enterprises.
The first civil war hence resulted in a sort of stalemate, which nevertheless allowed Cundinamarca to organize an expedition against the royalist regions of Popayán and Pasto, and Quito in July 1813.
Nariño assembled his 'Army of the South,' numbering 1500 to 2000 men, and managed to capture Popayán in January 1814, but was then defeated by the Royalist forces in Pasto, after which he was arrested in May 1814, and then sent to the Royal prison at Cádiz.
[2] By mid-1815 a large Spanish expeditionary force under Pablo Morillo had arrived in New Granada, which bolstered earlier royalist advances made by Santa Marta.
Morillo laid siege on Cartagena in August and it finally fell five months later in December with the city suffering large numbers of civilian casualties due to famine and disease.