Initially, Fort Borbón was established as a guard post by order of King Carlos IV of Spain with the purpose of withstanding attacks by the natives and the Portuguese on the lands under Spanish jurisdiction.

The governor of the province of Paraguay, Joaquín Alós y Brú, ordered the establishment of two forts in the north: Borbón and San Carlos del Apa to restrict the advance of the cavalry.

The Spanish tried to gain the friendship of the caciques (chiefs of the tribe) mbayás but they attacked Villa Real de Concepción in 1796, and because of it the military forces in the village massacred the families of the natives settled nearby, killing about 75 of them.

With the passing time, the interactions between the natives and the soldiers of Fort Borbón and Villa de Concepción became friendlier, and the authorities of Asunción signed temporary peace treaties with Chief Lorenzo.

Once the news of the war in 1801 between Spain and Portugal became public, Governor Lázaro de Rivera proposed pointlessly to take the Portuguese fort of Coimbra and settle more to the north in the lands of the Spanish Crown.