These birds are generally monogamous but not always faithful to their partner. In the western part of their range, they often hybridize with theLazuli Bunting. Nesting sites are located in dense shrub or a low tree, generally 0.3–1 m (1–3 ft) above the ground, but rarely up to 9 m (30 ft).The nest itself is constructed of leaves, coarse grasses, stems, and strips of bark, lined with soft grass or deer hair and is bound with spider web. It is constructed by the female, who cares for the eggs alone. The clutch consists of one to four eggs, but usually contains three to four. The eggs are white and usually unmarked, though some may be marked with brownish spots, averaging 18.7 × 13.7 mm (0.7 × 0.5 in) in size. The eggs are incubatedfor 12 to 13 days and the chicks are altricial at hatching. Chicks fledge 10 to 12 days after hatching. Most pairs raise two broods per year, and the male may feed newly fledged young while the females incubate the next clutch of eggs.
The Brown-headed Cowbird may parasitize this species. Indigo Buntings abandon their nest if a cowbird egg appears before they lay any of their own eggs, but accept the egg after that point. Pairs with parasitized nests have less reproductive success. The bunting chicks hatch, but have lower survival rates as they must compete with the cowbird chick for food.