A large number of the inhabitants moved only a few kilometres into a new settlement founded on the Lech and took the name Schongau with them in the 13th century.

In the Middle Ages, it was an important hub and commercial centre on the Verona-Augsburg-Nuremberg route and on the salt road from Berchtesgadener Land into the Allgäu.

When the last Staufer ruler Conradin moved to Italy in 1267 to defend his power against Charles of Anjou, his ally Duke Ludwig II of Bavaria unexpectedly denied his help and demanded the payment of debts, which is why Conradin had to give away a large part of his possessions as the Duke of Swabia (called the Konradinian donation).

[3] In this way, the Bavarian dukes of Wittelsbach, who were ambitious to extend their influence into the Alamannian settlements up to Lech, came to rule the Lechrain in 1268.

On 22 May 1493, a devastating fire destroyed large parts of the Oberstadt (upper town) and the ducal palace; it was not until 1514 that reconstruction was completed.

[4][5] Schongau was involved several times in martial conflicts and was often a transit camp for friendly and hostile troops.

As a result, the city became so poor that significant buildings such as the castle and balehouse fell into partial decay or were demolished.