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They will steal the food in the traps. I had success by using a hot glue gun to glue sunflower seeds to the cage or mousetrap. We have caught over 50 chipmunks in the past 2 months. It works great in the live cages.
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Will the chipmunks tunnel outside of the treated area and still be able to get into the garden? Also, I have raised beds and am concerned about them tunneling under the beds even with the area around the bed being treated.
Though it may seem odd try sprinkling paprika on the area, most garden intruders do not like the taste.
Rodents, like chipmunk can often be pests to your garden flowers and plants. This is a page about chipmunks attacking my plants.