Upvote:1
If you have booked two, completely separate tickets, you can ask at check in to have them 'tagged to the final destination.' If both of your tickets are on one reservation, with one Passenger Name Record, that makes it easier and you shouldn't have a problem checking bags through.
If completely separate, with your first leg on an airline such as Turkish, it should not be difficult, but you need to request this. You may want to arrive early at your departure airport, since the check-in agent at needs to be able to print baggage tags that conform to the interline agreement and get your bags to your final destination.
Aegean has online check-in from 48 hours up to 30 minutes before flights, via computer, tablet or smartphone from aegeanair.com or Aegean apps on Google and Apple stores.