Father Fernández de Santa Ana was born Benito Fernández y Rana at Berán, in the province of Orense, Spain, on June 4, 1707. He entered the Franciscan order and was ordained a priest, probably in Spain; shortly afterward he was sent, in 1731, as a member of the College of Santa Cruz de Querétaro, to San Antonio de Valero Mission in Texas. Between the Rio Grande and Mission San Antonio on June 25, 1731, a band of Apache Indians robbed him and Brother Estevan Zaes Monge of all their baggage and horses and killed two of the five soldiers who accompanied them. Three years later, at the age of twenty-seven, Fernández succeeded Father Gabriel de Vergara as president of the Texas missions of the College of Querétaro and the principal missionary at Nuestra Señora de la Purísima Concepción de Acuña Mission in San Antonio.
In 1739 the Canary Islanders in the villa of San Fernando obtained from viceroy archbishop Juan Antonio de Vizarrón y Equirreta a decree permitting them to hire mission Indians on their farms. Father Fernández wrote a memorial in which he refuted false statements and accusations made in the petition of the Canary Islanders, and as a result in 1741 the viceroy Duque de la Conquista revoked the decree of 1739. However, in 1743–44 two agents sent to Mexico by the cabildo of Villa de San Fernando succeeded in having a second decree, similar to the one of 1739, issued by Viceroy Conde de Fuenclara. Fernández then appeared in person before this viceroy in January of 1745 and persuaded him to rescind the decree of 1744.
After a severe epidemic in 1739, Fernández began the construction of permanent buildings of stone and mortar at Concepción Mission, including the twin-tower church that is still standing. To Father Mariano de los Dolores y Viana's project of founding three new missions, with a presidio, on the San Xavier (San Gabriel) River, Father Fernández gave his full support, despite persistent objections by the governors and presidio commanders in Texas (see SAN XAVIER MISSIONS). After Dolores y Viana had officially founded Mission San Francisco Xavier in 1748, Fernández personally founded San Ildefonso and Nuestra Señora de la Candelaria missions in 1749. To correct the misstatements in a report of Governor Pedro del Barrio Junco y Espriella, Fernández made a second trip to Mexico City and successfully presented to Viceroy Conde de Revillagigedo a long memorial, of fifty-nine sections, on November 11, 1749. In February of the following year he also presented his plans for the establishment of Apache missions on the Pedernales River, which included the transfer of San Antonio de Béxar Presidio to this river. Though his plans were not accepted, they led to an investigation that culminated in the choice of the San Saba River for an Apache mission with a new presidio.
Like his predecessor, Vergara, Fernández had always disapproved of military punitive campaigns against the Apaches as a means of putting an end to their raids. He believed that, like the other Indian groups, the Apaches could be induced to settle in missions, and that this would be a more effective means of establishing peace in Texas. He deplored the enslavement of Apaches who were taken prisoner in Capt. José de Urrutia's campaign in 1739, and after the campaign in 1745, in which he accompanied Capt. Toribio de Urrutia, he asked the viceroy to turn the Apache prisoners over to him, "so that they can help me to win the others." Though the fear of their enemies, the Comanches, was one reason why the Apaches finally agreed to a peace treaty with the Spaniards on November 28, 1749, this achievement was due in great measure to the consistent conciliatory policy of Father Fernández.
Shortly after February 1750 Fernández became ill and had to retire to the college in Querétaro, and Father Dolores was appointed his successor as president of the Texas missions. Fernández died at the college in late March or early April 1761. News of his demise was received at the College of Nuestra Señora de Guadalupe de Zacatecas on April 12, 1761. See also FRANCISCANS, SPANISH MISSION SYSTEM.