King Carlos II of Spain named Zúñiga Governor and Captain General of Spanish Florida on January 30, 1699.
The oath of office with instructions concerning the responsibilities of his appointment was administered by the court of the Casa de Contratación (in English: House of Trade) in Seville, on May 20, 1699.
He was given a license to carry four slaves, and he sailed to New Spain in the fleet commanded by General Manuel de Velasco y Tejada on May 23, 1699.
In 1701, he appointed Juan de Ayala y Escobar as "visitador general" of Apalachee to investigate the terms of the peace that the native tribes there had made with other peoples, such as the towns of Apalachicola Province.
[2][3] Zúñiga y la Cerda ordered the remaining Spanish missions in Apalachee and Timucua Province to be moved closer together for defensive purposes.