Thank you for contacting Ask An Expert.
Your question elicited a "snort" from me as I had just come inside the house to rant about the chipmunks AGAIN digging in my pots, this time uprooting my already struggling caladiums! The struggle against these pests for gardeners and homeowners is real. A friend calls the "rats with good PR" because they are so cute.
They love newly planted pots because the potting mix is soft, bare and easy for them to deposit their seed haul. I'm attaching some links which may help you.
What I would recommend first is to make your yard less desirable to them. I no longer feed the birds seed in the summer. I only feed them in the winter when the chipmunks are not active. If you do have a bird feeder clean up spilled seed on the ground. Fencing is of minimal use. For your containers and new plantings you can put down hardware cloth on the soil surface. A layer of fine gravel (chicken grit) may make the soil less desirable . Milorganite has been used and seems to have some effectiveness in repelling them probably due to it's odor. There are some commercial sprays available and it you choose to try them please follow the label directions.
Trapping via live or snap traps (or other killing trap) is probably most effective. Keep these away from children. Check live traps often. There is advice in the links above.
Overall if you can reduce their food source you will have fewer chipmunks and those that you do have will have less seed to bury which is the reason they are digging.
If none of these work perfectly, be ready to replant uprooted plants and try to enjoy the antics of the cute little buggers. This is advice I try to follow!