The 2010 Olympic 10km normal hill champion has been consistent all season with his worse finish being fifth from round six.
But he could still only boast one victory from round three in Finland, but doubled his season tally in Germany as he held off the challenge of Japan's Akito Watabe.
Lamy Chappuis was fifth after the ski jump, two places behind Watabe, but was third-quickest in the cross-country to claim victory by 1.9 seconds from his Japanese rival.
Norway's Magnus Moan was quickest in the cross-country section but could only manage tenth in the jump meaning he had to settle for third, 4.9 seconds behind Lamy Chappuis.
Lamy Chappuis sits pretty at the top of the overall World Cup standings on 455 points, with Moan second on 383.
Watabe's second place in Schonach was his first podium finish of the season and propelled him into third overall on 229 points, level with German Eric Frenzel who was fifth in front of his home fans.