From 1638 to 1642 (Kan'ei 15-19), the third Tokugawa shogun Iemitsu invested 7,000 ryō in the reconstruction of Nangū Taisha, which had been destroyed at Sekigahara. Designed by the shogunate's master carpenter Kōra Munemasa in the distinctive 'Nangū-zukuri' style, the eighteen structures including the main hall, worship hall, drum tower, two-story gate, corridors, and stone arched bridge were constructed, all now designated National Important Cultural Properties.

Ishida Mitsunari, leader of the Western Army, deployed Mōri Hidemoto and Kikkawa Hiroie at Mt. Nangu before the Battle of Sekigahara. Mitsunari's strategy called for the Mōri forces to attack the Eastern Army from behind, but Kikkawa Hiroie's secret pact with the Tokugawa side kept the Mōri immobile, sealing Mitsunari's defeat. The shrine's destruction was an aftermath of this battle.

During the Battle of Sekigahara in 1600, the Western Army commander Mori Hidemoto set up his headquarters within the precincts of Nangu Taisha. The Mori forces remained inactive throughout the battle — condemned as 'fence-sitting on Nangusan' — but the shrine was destroyed as the surrounding area became a battlefield.