In 1581, he took part on Tenshō Iga War, he was one of several general who led Nobunaga's troops in the Siege of Hijiyama.

The following year In 1582, Akechi betrayed Oda Nobunaga and took his power and lands, but was defeated two weeks later at the Battle of Yamazaki.

Barely surviving the battle, he hid on a nearby uninhabited island and lived by eating seaweed until the enemy withdrew.

Despite his actions, he was unable to counter Admiral Yi Sun-shin, whose naval activities effectively cut off Japanese naval supply lines to the Korean Peninsula; despite this failure and the ultimate defeat of the Japanese forces during the campaigns, Wakisaka's reward for participating in this war was an increase in territory to 3,000 Koku.

On October 21, during the decisive Battle of Sekigahara, Wakisaka switched sides along with Kobayakawa Hideaki, he defeated Ōtani Yoshitsugu's force, and contributed to the Tokugawa victory.