If you choose to stay in the waiting area, you will only have to pass through the security check before boarding your aircraft. Swiss-Passengers who are travelling within the Schengen area can proceed directly to the departure gates to board their transfer flight.
If you are travelling within the Schengen area, when you enter Switzerland you are no longer required to go through passport control. In any case, you must be in possession of a valid travel document recognized by the Swiss authorities. In addition, a visa is required in certain cases. You'll find more information here: The Federal Department for Foreign Affairs (FDFA).
Passengers travelling between countries that have signed the Schengen Agreement will no longer be required to pass through passport control. The countries concerned are
Passengers coming from or flying to countries that have not signed the Schengen Agreement have to pass through passport control at Zurich Airport.
Passengers arriving from a non-Schengen country and transferring to a Schengen member state, or vice versa, also now have to pass through passport control in Zurich. Your gate will be displayed on the flight information screen not later than 60 minutes before departure.