Mission San Bernardo, the third mission of the San Juan Bautista mission complex at the site of present-day Guerrero, Coahuila, was begun early in 1702. It was founded "two musket shots" north of San Juan Bautista Mission, which at that time formed the heart of the settlement that became Guerrero. Fray Alonso González, recently arrived from the missionary College of Santa Cruz de Querétaro, assumed the ministry, gathering three rancherías of Coahuiltecan Indians of the Ocán, Pacuache, and Pacal groups to number 400. In the mission's early days, as many as forty children were presented for baptism at one time, with soldiers of Presidio de San Juan Bautista and their wives serving as godparents. Despite several proposals to move the mission, San Bernardo remained within a league of the site of its founding until final secularization in 1829. Ruins of the mission church begun in the 1760s but never finished still stand just north of Guerrero, virtually the only visible remains of the Rio Grande missions. Martín de Alarcón, governor of Coahuila, was the first to propose moving San Bernardo. After his inspection of 1706, he advocated transferring it to the Frio River in Texas. That same year a smallpox epidemic depopulated the missions. An expedition was made to the Nueces River the following year to seek new converts and to punish Indians responsible for recent raids. In 1715 the Indians of San Bernardo and San Juan Bautista rebelled over treatment by the presidial soldiers. Fray Isidro Félix de Espinosa, who was serving at San Bernardo at the time, gives an eyewitness account of the episode in his Crónica. When Fray Miguel Sevillano de Paredes inspected the missions in 1727, San Bernardo had 200 Indians, of whom 165 were considered faithful Christians and 35 were being instructed in the catechism; 156 adults had been baptized, and 30 children had received the sacrament before dying. There was a "beautiful" church, with suitable furnishings and altar adornment. The pueblo consisted of five flat-roofed houses and sixteen of adobe and thatch. Yet the mission had never been able to produce an adequate corn crop for want of a reliable source of irrigation water. Because of the lack of corn, the natives had often returned to the wilds. That year an aqueduct had been run from the Nogal River, a dozen leagues or more away, but so far it reached only the outlying fields. An orchard and garden provided fresh fruits and vegetables. The twenty cattle given the mission in the beginning had suitable increase. Progress, however, had been disappointing.
At midcentury, proposals were heard to suppress the Rio Grande missions so as to give succor to those recently founded on the San Gabriel River in Texas. Only failure of the latter spared the older settlement. In 1756 the inspector Fray Francisco Xavier Ortiz, looking toward reduction of the Apaches and Comanches, proposed suppressing San Bernardo and San Juan to turn the cost of their maintenance to making new conversions. Failure of Santa Cruz de San Sabá Mission, founded for the Apaches and destroyed by the Comanches and their allies, canceled the plan. The inspector noted that the San Bernardo church was in poor condition, but new mission facilities were being built at a better site a league away. The missions were threatened again in 1762, when Fray Diego Jiménez, president of the Rio Grande missions residing at San Bernardo, and Fray Joaquín de Baños, the San Bernardo minister, joined in a new missionary undertaking for the Apaches. Both had been among the founders of the San Sabá mission in 1757. They now joined with Felipe de Rábago y Terán, commandant of the Presidio de San Sabá, to renew the effort with the Apaches on the upper Nueces River. Their efforts to sustain the Nueces missions, San Lorenzo de la Santa Cruz and Nuestra Señora de la Candelaria, from the resources of San Bernardo and San Juan Bautista put the older missions in jeopardy. But once again the new undertaking failed, while the older ones survived. As an alternative to secularization, San Bernardo was transferred in 1772 along with San Juan to the province of Jalisco. The Queretaran missionaries withdrew. Left unfinished was its grand new limestone church begun by Jiménez. The ruins visible today attest to Fray Juan Agustín Morfi's 1777 description of "a beautiful temple that would shine in any community [but] out of proportion to the place." Still serving as the mission church was a small, dark "canyon" of adobe with unadorned altar. Yet Morfi viewed San Bernardo, its irrigation system long since completed, as the richest mission of the province, with the greatest number of Indians and the most fertile lands. Since its founding, 1,618 baptisms had been performed, with 383 marriages and 1,073 burials. But progress of the Indians in Christianity was "almost imperceptible." In 1781 San Bernardo and San Juan were transferred to the missionary college of Pachuca. San Bernardo's Indian population had declined to 103. Despite petitions from vecinos of the Presidio de Río Grande, who coveted the fertile mission fields, it withstood secularization until after Mexican independence. Division of the mission lands, decreed in 1826, was certified as complete on January 22, 1829.