The Ōtomo were saved by Toyotomi Hideyoshi's 1586-1587 Kyūshū campaign and were allowed to reclaim Bungo province as their territory.

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.

From the middle of the Edo period onward, the domain's finances became tight, and in 1830, the 12th daimyō, Inaba Terumichi, had debts exceeding 300,000 ryō.

For this reason, in 1831, his retired father, Inaba Hiromichi, who had retained political power behind-the-scenes, carried out somewhat rough reforms such as thorough fiscal austerity and new rice field development, as well as the abandonment of old debts and negotiations for grace periods for repayments.

In 1844, the domain supplemented its military by organizing a paramilitary force centered on farmers with rifles who had experience as hunters.