In 1780 he was promoted to lieutenant while stationed at the Presidio of San Carlos de Cerro Gordo, in the remote Big Bend Country.
In a letter to his mother in Mexico City, he proudly described the chapel and sent money to purchase "carmine, vermillion and other painting materials", garden and flower seeds, and to send any Dramas she can spare to read.
On May 19, 1792, Zúñiga was promoted to captain and assigned to the Presidio of Tucson, but had to wait until 1793 until his successor for San Diego arrived.
Zúñiga blazed a trail between Tucson and the Zuni pueblos in 1795, but Apache hostilities prevented that route from becoming well-traveled.
He had a previous son born 1783 as the result of an affair with Teresa Morillo, wife of an enlisted man, Manuel Nieto.