Different Last Names on Different Passports

Hello,

I am a dual citizen between the USA and and EU country. I am finishing my bachelors here in the US and planning applying for a masters in the netherlands.

I have different last names on each passport (each parent has a different last name), and I was wondering how this would affect the process of studying and working abroad. My bachelors will be granted to my American surname, but I want to apply to the MS program under my EU citizenship so I can qualify for the EU student tuition.

I have documentation to prove both surnames belong to me: my birth certificate from where I was born (EU last name and EU territory), proof my father was an EU citizen at the time of my birth, and my US report of birth abroad (American last name), and proof my mother was an american citizen at the time of my birth.

Does anyone know how the different surnames will affect my application process or getting a job? I figure people who have changed their surnames after marriage and then got another degree might know what i should do here. Any other advice regarding the situation would also be appreciated.

Thanks