The Onmyou Taisenki manga does not tell the same history as the anime. The story happens years before the events in the anime.

The main character, Yakumo (who also appears on the anime, as a teenager) is the son of Monju, the chef priest of the Taihaku Temple, in Kyoto. Yakumo also trains the In, with a baseball ball. In this temple, a Toujinshi (闘神土, literally 'god of war'), and Monju's former teacher, Mahoroba, is imprisioned.

The problems start when Mahoroba escapes, gains power, and transforms Monju into stone. Yakumo is called by a Zero Drive, which was one of the treasures of the temple. This Zero Drive handles Byakko no Kogenta. The story of the manga is about Yakumo's first steps with a Shikigami, training with Idzuna (Taihaku Temple's shrine maiden) and seeking Mahoroba throughout various Japanese historical dates. Famous Japanese historical characters such as Oda Nobunaga also appear in the manga.