If my customer cancels their flight, can I do the refund from my portal myself?

Yes, in most cases you can start a flight cancellation and refund request from inside your portal, but what actually happens next is decided by the airline and the fare rules, not by the software. Your booking screen will normally give you a cancel option on the ticket, and that sends the request through to the supplier or airline system the ticket was issued on. The portal keeps a record of the request and updates the booking status so you and your staff can see where it stands.

What you get back depends entirely on the ticket your customer bought. Some fares are fully refundable, some refund only the taxes, and some are not refundable at all. Low cost airlines in particular often allow no refund once the ticket is issued. The portal shows you the rules that came with the fare at the time of booking, so it is worth saving or checking those before you promise anything to the customer.

Timing is the part nobody can guarantee. The airline has to assess the refund, the supplier then has to pass it back, and if your customer paid by card it has to travel back through the payment provider as well. Some refunds come through quickly and others sit for a long while. Certain airlines and certain fare types also still need a manual request handled by the supplier rather than an instant automatic cancellation, and your plan and the connections you use will affect which ones are automatic.

Before you cancel anything, open the booking in your portal, read the fare rules attached to it, and tell your customer clearly what is refundable and that the money comes back on the airline's timetable rather than yours.