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I am planning to visit France (the country that issued me my schengen visa)but I can only do that either through Malta or Athens as there are no direct flights so I would have to have a short layover in Athens for two hours or a self transfer in Malta for three hours (it is one ticket with a transit in either). In this case will I get the stamp from Athens/Malta or from my final destination in France.

user98132
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    Important is only that France will be the major part of your visit and that the whole stay inside the Schengen area conforms to the 90/180 rule. – Mark Johnson May 27 '19 at 08:27

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There are typically no immigration checks on flights within the Schengen area. Your passport and visa will be checked and stamped when you enter the Schengen area. The fact that this will be a different country than the one which issued your visa isn't a problem, lots of people arrive in the Schengen area with further connecting flights before their final destination.

The same thing applies on departure, you will only receive an exit stamp when you leave the Schengen area.

Note that while there are typically no immigration checks within the Schengen zone, occasional spot-checks are possible. You probably won't experience any of these, and you shouldn't expect to receive a stamp if you do.

Chris H
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