A method and system for the treatment of Monarch butterflies (Danaus plexippus Kluk (Lepidoptera: Nymphalidae) to protect them from various life-threatening conditions, including the negative effects of various pesticides, provides Monarch butterflies with the ability to assimilate and degrade pesticides such as neonicotinoids and fipronil. Certain embodiments involve the inoculation of flowers by honey bees with desired bacteria that are able to degrade pesticides, such that when Monarch butterflies visit such flowers, they are exposed to such bacteria, transforming the microbiome of the Monarch butterflies so that pesticides can be degraded, thus enhancing the health of the Monarch butterflies.