In the 1600 Battle of Sekigahara, he defected with a coalition of smaller feudal lords in southern Kyushu to the Eastern Army, and as a result was confirmed in his holdings under the new Tokugawa shogunate.

In June 1656 he donated a bell to the Imayama Hachimangu Shrine, which is the first written inscription of the name "Nobeoka" in place of "Agata".

As a result, Kiyozumi was demoted and transferred to Itoigawa Domain in Echigo Province with a reduction in status to 50,000 koku.

In 1692, the fudai daimyō Miura Akitaka was transferred to Nobeoka from Mibu Domain in Shimotsuke Province, but with a kokudaka of only 23,000 koku.

Despite his low kokudaka, he worked hard to settle the aftermath of the peasant uprisings, and to resolve boundary disputes with Takanabe Domain and Bungo Province that had continued for decades.

His son, Makino Sadamichi, rose through the ranks of the shogunal administration to become Kyoto Shoshidai in 1742, and some 30,000 koku of his holdings were widely scattered across Kawachi, Ōmi, Tanba, and Mino Provinces.

Nobeoka was then assigned to Naitō Masaki, who had been demoted from Iwakidaira Domain in Mutsu Province over a peasant revolt.

Successive feudal lords worked hard to reform the domain's administration, and in particular, the sixth daimyō, Masayori, forcibly confiscated the business privileges of merchants and strengthened the monopoly system.