What is organic honey? organic honey or raw honey comes straight from the beehive. The beekeeper will usually filter the honey to remove small debris and bugs, including pollen, beeswax, and parts of dead bees. Organic honey will have a USDA certification stating that the beehive is free of chemicals. What is natural honey? Here, the honey is collected by bee farmers and packaged for consumer use. From the point of collecting the honey and then selling it in the store, a series of processes are involved. This can change the organic state of the honey. Hence, no USDA certification will be there for natural honey. Things that make organic honey different from other honey