I am a dual citizen (US/Greece) currently living in the US and visiting Greece for three and a half months. I entered Europe through Germany using my US passport (the Greek one is in the process of being renewed) and was told I could only be in the Schengen area for 90 days.
Am I legally allowed to stay in Greece as long as I’ve planned (~105 days), given that I’m a Greek citizen? How do I justify this to officials when returning to the US?
You're a Greek citizen. You can stay in Greece as long as you wish. If you're asked about it when you leave, just show your Greek passport.
As a Greek citizen, you have the right to stay in the EU for as long as you like.
However, you would probably still be well-advised - once you have your Greek passport back - to leave the Schengen zone using your US passport before your 90 days are up, and re-enter using your Greek passport.
The risk if you don't is that if you pass Schengen immigration using your US passport in the future - particularly if you do not have your Greek passport at the time - the immigration agent will check your stamp dates and assume that you overstayed. Which is likely to lead - at least - to awkward questions.
