Yoshimune officially succeeded his father Sōrin in 1576 and authorized the campaign to expel the Shimazu clan from Hyūga province.

After the Ōtomo army was defeated in the Battle of Mimigawa (1578), Yoshimune was forced to maintain order within his clan due to the growing number of rebel vassals.

In 1587, after Toyotomi Hideyoshi's main forces invaded the island of Kyūshū and defeated the Shimazu, Yoshimune was confirmed as Bungo's daimyō.

In 1592, He led 6,000 men to Korea who were part of the army under the leadership of Kuroda Nagamasa, but showed cowardice in the fighting around Pyongyang: learning that a considerable Chinese force was moving in the area, Yoshimune ignored Konishi Yukinaga's request for help and he even withdrew from the countryside, an event that caused Wrath of Hideyoshi, who took the lands from the Ōtomo.

His son Yoshinobu (died 1639) served Tokugawa Ieyasu as a simple samurai and distinguished himself during the Siege of Osaka.