Josef de Zuniga was born in Mexico in 1755. He entered service as an officer candidate in the frontier army at the age of 17 enjoying the position of soldado distinguido, which qualified him as a nobleman, not subject to the performance of manual labor or other less distinguished tasks. In 1778 Zuniga became alferéz (sub lieutenant) after extensive service on the Texas frontier. By 1780 Zuniga was promoted to lieutenant while serving at the Presidio of San Carlos de Cerro Gordo in the Big-Bend Country of Texas.
In 1781 Zuniga was recruited by Captain Rivera y Moncada to lead a division of colonists from Guaymas to Loreto and Bahia San Luis Gonzaga by sea. The colonists, destined to found Pueblo de Los Angeles and the Santa Barbara area, were escorted by Zuniga from the Baja Peninsula to San Gabriel Mission.
In September of 1781, Lt. Zuniga was appointed as the second comandante of the Presidio of San Diego. Lt. Zuniga relieved José Francisco Ortega who had served as comandante of San Diego for 8 years. Alferéz José Velásquez was Zuniga's second in command until he passed away in 1785. During Zuniga's 11 year tenure as the military commander of San Diego he built and extensive comandancia (house of the commandant) and maintained good relations with his fellow soldiers. He kept good accounts and related well with superiors, missionaries, and the local Indians. In 1783 he built a "beautiful church" at the presidio. He served as carpenter, mason, and painter for the construction of the chapel. In 1784 he received membership in third order of Franciscans.
By 1792 Zuniga had been promoted to captain and assigned to the royal presidio of Tucson. Having to wait for his replacement, he served on detached duty at Monterey and finally arrived in Tucson in 1794. Zuniga served as comandante of Tucson until 1806. Later he ended his career as a lieutenant colonel and as Adjutant Inspector of Presidios in Arizpe, Sonora.