Can the flight booking API give me the airline's own booking reference so my customer can check in with the airline?

Yes, in most cases the flight booking API returns the airline's own booking reference once the reservation is confirmed, and you can pass that on to your customer for check in.

It helps to know that a booking usually has more than one reference. There is the reference your own system creates so your staff can find the booking, and there is the airline reference, a short code of letters and numbers that the airline holds in its own records. Airline websites and airline apps ask for the airline one, together with the passenger surname exactly as it appears on the ticket. Most agencies store both against the booking and print the airline reference on the confirmation they send out, so the customer has it in hand when check in opens.

There are a few things to be honest about. When a journey uses more than one airline on separate tickets, there can be a separate reference for each airline, and the customer may have to check in with each one in turn. The point at which the airline reference becomes usable can also vary, because with some airlines it only works on their site after the ticket has been issued rather than at the moment the seats are held. Exactly what is returned, and how quickly, depends on the airline and on the supplier connection behind your account.

The next thing to check is whether your booking confirmations and your portal already show the airline reference alongside the lead passenger surname, and if they do not, ask for it to be added so your staff are not looking it up by hand every time a customer calls.