The plot involves a beer or lager being continuously brewed and tapped at various heights in the vat. the bottom level has special powers. The wilds outside the towns are inhabited by mythical creatures.
It's "The Drawing of the Dark" by Tim Powers.
From the Wikipedia entry:
The year is 1529, and Brian Duffy, a world-weary Irish mercenary soldier, is hired in Venice by the mysterious Aurelianus to go to Vienna and work as a bouncer at the Zimmerman Inn, former monastery and current brewery of the famous Herzwesten beer.
- Fantasy medieval novel set in alpine Europe - check.
As it turns out, Aurelianus knows more about Duffy and his past than Duffy himself knows, and his real purpose in hiring him is to protect the hidden Fisher King, secret spiritual leader of the western world, and to defend him and the West against the Turkish advance. And the real reason that Vienna must not be captured by the Turks is that it is the site of the Herzwesten brewery. Its light and bock beers are famous throughout Europe, but the dark beer, produced only every seven hundred years, has supernatural properties and must not be allowed to fall into enemy hands.
- Beer with supernatural powers - check.