Del Junco started his career as a conquistador in the 1526 expedition led by Sebastian Cabot exploring the Río de la Plata in present-day Argentina.
Del Junco was named second in line of succession, after Gonzalo's brother Hernán, in the event of the death of the first governor of the New Kingdom of Granada.
[6] The conquest expeditions of Juan del Junco commenced in 1526, when he embarked on a ship leaving Sanlúcar de Barrameda.
[3][11] Juan del Junco is noted as one of the captains of the newly founded New Kingdom of Granada to hand back the weapons of the earlier dismissed Lázaro Fonte, lover of Zoratama.
[13][14][15] After the conquest expeditions, captain Del Junco was appointed a regidor (councillor) of Santa Fe de Bogotá,[16] and received the encomienda of Cucaita, in the province of Tunja.
[9] In a 1560 letter, Juan del Junco wrote to the Spanish Crown "of the 11,000 indians that resided on the banks of the Magdalena River, not even 500 survived".