It is natural and normal for your pet to relieve themselves in the crate during the flight. Make sure you line the crate with an absorbent mat or puppy pads to soak up the urine. All Petraveller crates are lined with super absorbent and washable Petraveller Sky Beds to ensure your pet's flight is comfortable.
What to do if your dog poops on a plane?
What if my emotional support dog suddenly poops or pees on a 10-hour flight? Then you clean it up and apologize to your stewards and your surrounding fellow passengers. This is of course assuming she is flying in cabin. If she is in cargo there is sadly not much to be done until you land.