The San Juan complex stands as an example of the difficulties faced by the Spanish in maintaining a number of competing missions in the San Antonio area. The long rectilinear plan of the compound never seems to have been fully developed. The mission church was never completed, with only its side aisle serving as a chapel in its place. The present church is highlighted by its two tiered espadaña, or belfry, set at one end of an otherwise austere facade punctuated by buttresses supporting the arcade that would have formed one side of the church. The interior of the chapel, with exposed timber roof beams and purlins, features a modern altar, with four Solomonic columns. The central statue on the altar is of St. John Capistran, the patron saint of the mission, and the statue is believed to be of eighteenth-century origin.