Chania uses a single smaller, modern-looking terminal, which is very easy to navigate. The distances to the planes are short, expect larger crowds in the summer season in a relatively small area.
Check-in for flights into and out of the Schengen area is in a common lobby. Check-in takes place after the common security checkpoint, with some gates after passport control while others are not.
The departure and arrival halls are on the ground floor.
The airport closes between the last and first arrivals, usually opening hours are 4:00 to 0:00.