Life Cycle Assessment (LCA) has been increasingly used for the improvement of the environmental performance of products and services, including agro-food chains. Pollination by honeybees can be regarded as one of the functions of an apicultural system and is of utmost importance for both natural ecosystems and agriculture. Furthermore, the beekeeping chain can represent an instrument for the protection and conservation of honeybee diversity when local subspecies are used. The Carbon Footprint of honey evaluates greenhouse gas emissions throughout the Life Cycle Assessment—more specifically, emissions of carbon dioxide, nitrous oxide, and methane. To this aim, data from beekeeping farms were collected, including data on annual honey production, other hive products, the geographical locations of the apiaries, processing plants, technologies used, and fuel and energy consumption. Based on the ISO 14040 method for the use of Life Cycle Assessment, the Carbon Footprints that were calculated for honey ranged from 1.40 to 2.20 kg CO2e/kg of honey for migratory beekeeping and from 0.380 to 0.48 kg CO2e/kg of honey for non-migratory beekeeping. The movements for the management of migratory beehives (on average, 44 km/hive for farm 1, 32 km/hive for farm 2, and 13 km/hive for farm 3) represented the main impact in migratory beekeeping systems, and they were quantified as 1.234, 1.113, and 0.68 CO2e/kg of honey. However, electricity represented the main impact of systems without migratory practices.