After finishing second and third in the opening two World Cup events German Moeller had failed to reach the podium in the subsequent two events.
But the 30-year-old changed all that in style on home ice as he recorded a total time of 1:39.526 minutes for the win.
Russian Albert Demchenko was second, 0.064 seconds behind Moeller, while Italian Dominik Fischnaller was third, pushing Felix Loch into fourth – the first time this season the German has failed to finish on a World Cup podium.
Despite his worst result of the season Loch holds on to his overall World Cup lead as he sits pretty on 415 points, with compatriot Andi Langenhan second on 350 after finishing sixth in Konigssee.
Moller is now third overall after his maiden victory of the season, one point ahead of Demchenko.
There was more to cheer for the home fans in Konigssee as Germany's Johannes Ludwig set a new start record of 3.259 seconds, but he could only finish ninth.