Every gardener likely has a story about squirrels or chipmunks (or maybe even both) making a nuisance of themselves. Here's how you can stop squirrels and chipmunks from eating flowering plants, vegetables, and fruit in your garden. 1. Understand Why Squirrels and Chipmunks Dig As exasperating as squirrels and chipmunks can be, there are several things we can do to coexist on more friendly terms. First of all, think about why these creatures do what they do.