If my customer cancels, can I refund their money back to their card from inside the system or do I have to do it separately with my payment provider?

Yes, in most cases you can start the refund from inside your travel agency software, but whether the money actually moves on its own depends on the payment gateway you use and on the supplier behind the booking.

The usual flow is that you cancel the booking first, and the airline, hotel or supplier confirms what is refundable after their penalty. Your software records that amount against the booking so your accounts and your customer ledger stay correct, and then you raise the refund to the customer. If your payment gateway allows refunds to be triggered through its connection, you can send the refund straight from the booking screen and the status updates by itself. If the gateway does not support that, or if your customer paid you by bank transfer, cash or cheque, the system will still let you record the refund and keep the paper trail, but you will have to pay the customer out yourself.

Be realistic about timing. Getting a refund approved by an airline can take weeks, and some suppliers settle it as a credit to your account rather than sending money back for each booking, so the refund you owe your customer and the money you receive do not always arrive together. Most setups also let you hold back your own service fee and refund only the balance, as long as your terms say so clearly.

The next thing to check is whether your payment provider allows refunds to be triggered through its connection rather than only from their own panel, and then ask us which of your suppliers return a refundable amount automatically so you know where manual follow up is still needed.