The best method for killing carpenter bees is to use an insecticide dust in and around their nests. Many commercial traps are available that can kill carpenter bees more naturally without using harsh chemicals or poisons.
If using an insecticide dust, one application should be sufficient if the dust is applied as soon as the adults emerge to mate in the spring. However, if the females have already laid eggs before the insecticide is applied, an additional dusting may be needed in the fall to effectively kill the juvenile bees after they hatch.
After insecticide has been applied, the holes the bee created in the wood should be sealed using wood putty, caulk or another commercial sealant. Most pest control experts recommend waiting at least a few days between using the insecticide and sealing the hole. This time ensures that all of the bees are exposed to the insecticide because any remaining bees unaffected by the chemicals would otherwise move on and drill another hole in the wood.
It is best to apply the insecticide in the evening because this is when the bees are less active. This reduces the chance of being stung by a female trying to defend her nest.