In 1759 Rafael Martínez Pacheco, presidio commander and government official, petitioned the viceroy of New Spain for a post in Texas, where he said he had had experience in helping Diego Ortiz Parrilla move the San Francisco Xavier de Gigedo Presidio from the San Marcos River to the San Saba in 1757. Martínez claimed to have recruited families to settle at San Saba and to have served as conductor of supplies and horses for San Antonio de Béxar Presidio. On November 23, 1763, he was appointed commander of San Agustín de Ahumada Presidio, on the lower Trinity River. His inadequate work and failure to report antagonized Governor Ángel de Martos y Navarrete, who ordered the removal of the presidio to Los Horconcitos and eventually ordered Martínez's arrest. In the ensuing conflict the presidio was burned, and Martínez fled to La Bahía and San Antonio. Hugo Oconór, who came to San Antonio in 1765 to investigate the matter, found Martínez Pacheco not responsible for the trouble and returned him to his presidio. He arrived at the Trinity on September 28, 1769, and began an efficient administration of his post. In the fall of 1769 he was made responsible for delivering to the French post at Natchitoches a group of English, German, and Cajun families who had been shipwrecked near La Bahía.
After the abandonment of San Agustín de Ahumada in 1770, Martínez became commandant of Nuestra Señora de Loreto Presidio at La Bahía. On November 8, 1772, he made a lengthy report on the condition of Texas missions, in which he blamed their state upon incompetent and grasping governors and presidio commanders. On December 5, 1786, he was appointed governor ad interim of Texas. In October José Mares reported to him on his trip from Santa Fe. In 1789 Martínez aided Juan de Ugalde in expeditions against the Apaches and barely escaped assassination in San Antonio by a group of visiting Lipans. His removal as governor was approved by the viceroy on October 18, 1790.