ABSOLUTELY ! Shut them in the chicken house and securely close the door(s).
I have a 5' chain link fence with hardware cloth on the bottom 2ft. around my chicken run but a racoon can climb pretty well. Am thinking I should maybe have put metal siding along the bottom instead.
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It is far less work and trauma to close a door than wake up to a bunch of dead chickens like many here have. Even the best constructed runs have failed to stop a predator.
To be completely honest, I'd even be worried about that kind of run during the day. The holes in the chain link fence are really wide, and things can dig under it.