Once a female has chosen a mate, she alone builds the nest. The nest is composed of strips of juniper bark, rootlets, grasses, cobwebs, cocoons and may be lined with hair from animals. Although nests have been found in various trees, the one factor they have in common is the presence of strips of juniper bark. Once juniper reaches an advanced age, strips are easily taken from the bark and used in nest building. It appears that female Golden-cheeked Warblers are unable to build nests without this resource, which makes the presence of oldgrowth Ashe juniper vital to the species' survival.
Incubation begins one day before the last egg is laid.
For approximately the next 12 days, the female warbler incubates the eggs. The male is for the most part inattentive at this time, joining the female only when she forages for insects away from the nest. To avoid attracting the attention of predators, eggshells and fecal sacs of the young are either carried away or eaten by the adults. The nestlings fledge at 9 days but remain near the adults for approximately 4 weeks, begging for food. By the third week, the young birds are foraging for themselves and can fly as well as the adults.