/u/kieslowskifan has an excellent comment on Berlin that answers this question

Both Germany, generally, and Berlin, specifically, were divided into four occupation zones (US, UK, France and USSR). This was intended to be a temporary measure until a peace treaty. However, it soon became clear that Germany would not be united. Stalin's position was that as there wound be "two Germanies and the Western Allies should accept that Berlin is the capital of East Germany" (at the time West Germany was considering Frankfurt as its capital). Berlin was surrounded by East Germany, and West Berlin was not technically part of West Germany - two good reasons why it would not be a good capital for West Germany. By contrast, the Eastern Bloc made attempts to get the West "to abandon the city such as declaring East Berlin the official capital of the GDR[.]" In fact, "Khrushchev dangled the idea that a unified Berlin would become a neutral free-city instead of a GDR [i.e. East German] capital."