However, Ōtomo Yoshimune (Sōrin's son) behaved in a cowardly manner during the Japanese invasions of Korea (1592–1598) which so angered Hideyoshi that he was deprived of his fief and banished.

In 1582 when Oda Nobunaga was assassinated at the Honnō-ji Incident, Toyotomi Hideyoshi was fighting the Mōri clan at Bitchū Takamatsu Castle and was forced to disengage and return to Kyoto post haste to deal with Akechi Mitsuhide.

After his return, he had a severe falling out with Ishida Mitsunari over his actions on Korea; however, he still remained loyal to the Western Army and led his forces at the Siege of Tanabe in 1600.

He defected to the Eastern Army shortly after the Battle of Sekigahara at the persuasion of Tōdō Takatora and through his intercession was relocated by Tokugawa Ieyasu to a 20,000 koku holding in Bungo Province in 1601.

The 6th daimyō, Mōri Takayoshi encouraged literary and martial arts, and worked to promote industry in order to rebuild the domain's chaotic administration.

He was noted for his intolerance of wrongdoing, and he expelled retainers from the territory or dismissed them from their posts.He laid the foundation for the later establishment of a domain academy, and also focused on disaster countermeasures.

The 8th daimyō, Mōri Takasue enforced three thrift edicts, halved the stipend of retainers of 200 koku or more, reduced expenditures, issued hansatsu bank notes.