The departure of La Mar and sending of Colombian troops from Quito and Bogotá to the borders of the department made the Cabildo of Guayaquil state that it supported a federalist constitutional reform, and temporarily suspended its autonomy, until the formation of a new constituent congress.

However, its political autonomy lasted until October 1827, when General Juan José Flores entered the city of Guayaquil with the Colombian army to restore constitutional order.

The Free Province of Guayaquil emerged after the proclamation of the Reglamento Provisorio de Gobierno (provisional constitution) on November 11 of that year as an independent state, which was not recognized during the war period.

The Colombian army, commanded by Antonio José de Sucre, merged with the Guayaquil troops, with certain Peruvian and River Plate elements, initiated the so-called Campaign of the South that concluded with the independence victory at the battle of Pichincha on May 24, 1822.

However, the city of Cuenca decided to annex itself to Gran Colombia on April 11, 1822; and the Quito authorities, after the battle of Pichincha, also made the decision to join the Colombian nation on Sucre's suggestion on May 29.

In the city of Guayaquil, there were three factions within the population and its authorities; there were those who preferred an annexation to Colombia, while others saw it more favorably for the territory to be part of Peru, and lastly, those who wanted the province to remain independent and autonomous, among whom were José Joaquín de Olmedo and other members of the Government Board.

Its status as the main port on the Pacific coast and its rapid commercial growth made Peruvian claims manifest through General José de San Martín.

The cities aspired to regain some control over the rural territory, they had held for much of the Colony and lost during the Cadiz regime; however, the creation of the 1824 law established a municipality in each canton head.

The protagonists of this feat were the brothers Juan Francisco and Antonio Elizalde, and also Marshal José Domingo de La Mar y Cortázar, who was appointed civil and military chief.

After the decision by the revolutionaries, the authorities representing the Colombian government, including General Tomás Cipriano de Mosquera and Colonel Rafael Urdaneta, who later became president of Gran Colombia, hastily left the city.