I'm flying from Brussels to Tallinn on the 7th September in LOT. I have a 2.5 hours layover in Warsaw.
Is there a possibility that I will be quarantined in Warsaw?
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Of course not, since you're leaving again in 2.5 hours. AFAIK there's not a single country that prevents you from catching a connecting flight due to quarantine.
Also, per the government website (LINK), those entering Poland from within the EU/Schengen don't have to quarantine.