Mission San Juan was a self-sustaining community. Within the compound, Indigenous artisans produced iron tools, cloth, and prepared hides. Orchards and gardens outside the walls provided melons, peaches, and pumpkins. Beyond the mission complex Indigenous mission farmers cultivated maize (corn), peppers, beans, squash, sweet potatoes, and sugar cane in irrigated fields. Over 20 miles southeast of Mission San Juan was Rancho de Pataguilla, which, in 1762, reported 3,500 sheep and nearly as many cattle.

These products helped support not only mission communities, but also the local settlements and presidial garrisons in the area. By the mid 1700s, Mission San Juan, with its rich farm and pasture lands, was a regional supplier of agricultural produce along the historic trading route, El Camino de Real de los Tejas.