Her third victory of the season so far continued the German dominance of the World Cup this season, with only fellow countryman Anke Wischnewski and Russian Tatiana Ivanova also claiming wins in the opening rounds.
Geisenberger led after the first run, recording 51.253 seconds and ensured it was going to be a golden weekend for Germany as she was also quickest on her second visit to the track as well for a combined time of 1.42.325.
Carina Schwab was second quickest overall, 0.317 seconds back, while Aileen Frisch ensured it was a German one, two, three in Konigssee.
Canadian Alex Gough, 0.398 seconds back from the winner, interrupted the German dominance, trailing home in fourth, with another of Geisenberger's fellow countryman, Wischnewski, back in fifth.
The top three positions remained unaltered after the first and second runs, with only Gough and Wischnewski swapping positions in their second attempt.