What happens if a customer pays on my website but the seat or room is gone by the time the booking goes through?

It does happen sometimes, and the usual result is that the payment is taken but no ticket or voucher is issued, so the booking sits in your system as failed or on hold until someone sorts it out. Airlines and hotel suppliers only hold a price and a seat for a short while during the search, and in busy periods another customer somewhere else in the world can take the last one in the seconds between your customer pressing pay and the supplier confirming.

A good portal will not pretend the booking succeeded. The customer should see a clear message saying the booking could not be completed and that the money will be returned or the trip rebooked, and the same booking should appear in your admin panel flagged for attention so your team sees it even if the customer does not call. Some portals will also try the search again straight away and offer the nearest alternative at the new price.

What happens to the money after that depends on your payment gateway and on the supplier. If the charge was only an authorisation it can usually be released quickly, but if it was fully captured the refund goes back on the same card and can take several working days to appear, and that timing is set by the bank, not by your website. Where the supplier has already taken the funds, you may have to raise the refund with them separately.

Ask your provider how failed bookings are shown to the customer and where they land for your staff, and check with your payment gateway whether it authorises first or captures immediately.