Beehive products have a rich global history. In the wider Levantine region, bees had a significant role in Egypt and Mesopotamia, and intensive beekeeping was noted in Israel during the Biblical period when apiaries were first identified. This study investigates the origins of this extensive beekeeping through organic residue analysis of pottery from prehistoric sites in the southern Levant. The results suggest that beehive products from likely wild bees were used during the Chalcolithic period as a vessel surface treatment and/or as part of the diet. These functions are reinforced by comparison to the wider archaeological record. While the true frequency of beeswax use may be debated, alternatives to beehive products were seemingly preferred as wild resources contrasted with the socio-economic system centred on domesticated resources, controlled production and standardization. Bee products only became an important part of the economic canon in the southern Levant several millennia later.