Adding 2 passports in APIS? Dual AU/US citizen flying EU->USA->Australia

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I'm a dual US & Australian citizen, currently living in Spain. I've got an upcoming flight on 1 PNR which is MAD-DFW-MEL (it was cheaper than flying via Asia or the Middle East)

I can only enter 1 passport into the booking APIS.

If I add my US passport details, it expects an ETA on my US passport to be allowed to travel to my final destination, Australia. This is not possible, as an Australian citizen. I can only use my Australian passport to travel to Australia.

If I enter my AU passport details, I'd need an ESTA for the flight to DFW. I can't apply for an ESTA on another passport as a US citizen. I can only use my US passport to travel to the US.

So I can't check-in online, but if I present both passports at the airport check-in, would they be able to enter both for each flight, or override the system?

I tried calling and asking but the agent said she couldn't help, just that it's up to passengers to ensure they have the right visas etc, so not really helpful.
 
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Thankyou that sounds simple enough, just do it the old fashion way (before online check ins existed!).

My main concern is trouble at MAD about the connecting flight to Australia. But it sounds like they’ll just not give me the 2nd boarding pass and tell me to get it in DFW at one of the transit desks?

Being the US, I’d have to collect and recheck any bags regardless, so it won’t really cause any issues there.

Assume for the return I can put the US passport into the booking and check in online and get both boarding passes. Although my Spanish resident visa is linked to my Australian passport, the EU doesn’t care which passport I use and doesn’t (currently) have an ETA/ESTA-like requirement for non-citizens.
 
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