José Francisco Ortega was a native of the Zelaya, Guanajuato Province, Mexico. Enlisting in 1755, he began military service at Loreto. He married María Antonia Victoria Carrillo at Loreto in 1759. His service record of 1787 shows him as a private for 10 months, advancing to sergeant within 16 months. He served 16½ years as a sergeant and 14 years as a lieutenant.
Some time after making sergeant, Ortega left the army in favor of mining in Baja, where he became alcalde (mayor) of mining camps on the peninsula. Portolá, as governor, readmitted Ortega to the army as sergeant and put him in charge of the accounts of the royal warehouse.
José Ortega accompanied the first land expedition to Monterey in 1769 with Portolá. He was perhaps the 1st to discover and scout San Francisco Bay and was a tireless explorer and trailblazer. Ortega was a great favorite of the missionaries, especially Junípero Serra. By 1775 he was lieutenant in command at San Diego. Serving as comandante of San Diego for 8 years, Ortega founded the missions San Juan Capistrano and San Buenaventura.
In 1782 he founded the presidio of Santa Barbara, planning the fortifications, and irrigating works. Acquiring livestock for the presidio from Ventura, he established orchards, and began farming on a large scale at the presidio. Felipe de Goicoechea replaced Ortega as comandante of Santa Barbara in 1784. In 1787 Ortega was sent to command the presidio at Monterey, serving there until 1791. A year later he commanded the presidio in Loreto. Ortega retired in 1795 as a brevet captain attached to Santa Barbara with 40 years service in the army.
José Francisco Ortega moved to a ranch at Refugio in Santa Barbara about 1791. He died at the age of 65 while riding through the Indian village of Casil at Refugio beach and was buried at the Mission of Santa Barbara on February 3, 1798.