Catching separately ticketed flights through an airport without leaving the transit area

Question

I'm looking to fly from Istanbul, Turkey (IST) to Nairobi, Kenya (NBO) and then to Tel Aviv, Israel (TLV). By far the cheapest flights I could find are a round trip from Istanbul to Nairobi, and then a one way flight to Tel Aviv. The round trip and one way tickets would be through different airlines.

I am wondering what, if any, difficulties I will face changing planes in Istanbul, Turkey on my way back from Nairobi to Tel Aviv. This will not be a normal layover as I am used to with a single ticket purchase. I will need to check into my second flight to Tel Aviv, since that airline knows nothing about my connection. Would I be able to do this without leaving the international transit area of the airport? I would like to avoid the hassle and possible problems of going through immigration just to go to the airline ticket counter to retrieve a boarding pass.

Perhaps checking in online and print my boarding pass? Sometimes airlines still want you to check in at the counter or a computer kiosk before heading to the gate.

To make matters slightly easier, I will not be checking any bags. Also, I am a US citizen if that matters.

Right now it looks like the round trip ticket (Istanbul<->Nairobi) would be through Egypt Air and the one way (Istanbul->Tel Aviv) would be on Aegean Airlines.

Answer 1

IST has a sterile transit area and transit desks precisely for this purpose. From the official website:

Transfer Passengers:(International Transfer Passengers With An International Connection Flight)

A boarding card is issued for the passenger (if not issued in the country of origin) at the transit desk of the relevant handling company on the Arrivals floor. The passenger does not go through passport control. Instead, he/she directly proceeds through the transit area into the International Departures area. Baggage will be automatically transferred to the connecting flight.

The main problem will be checked-in baggage, which you probably cannot check through if you have two completely separate tickets, and which you will not be able to retrieve without going through Immigration and Customs. But if you can travel with carry-on bags only, and you don't need a Turkish visa or can get one on arrival (you will be asked at NBO when you check in), you should be gold.