Bee Nest generates naturally on oak or birch trees that spawn within two blocks of a flower, typically in meadow, plains, and flower forest biomes. Each nest houses up to three bees, which exit during the day to collect pollen and return to deposit honey. The honey level advances from 0 to 5 as bees make trips; at level 5 the nest drips visually.

Harvesting at level 5 with an empty bottle collects a honey bottle; using shears collects three honeycomb items. Both actions reset the honey level to 0 and anger nearby bees unless a campfire or lit fire is placed within five blocks directly below the nest. Bees become aggressive when the nest is broken without Silk Touch or without smoke nearby, stinging and applying the Poison effect.

Players use bee nests in honey farms by placing campfires, dispensers with bottles, and redstone timing to automate collection. Honeycomb crafts beehives, honeycomb blocks, and is used for waxing copper blocks to halt oxidation.