The Arima clan, which had governed the Shimabara peninsular for generations, left and moved to another domain.
After Toyotomi Hideyoshi's death, the House of Tokugawa established the Edo shogunate and began to exercise power over the feudal lords. Arima Harunobu ended up being sentenced to death, following an incident whereby he gave a bribe to one of the shogun’s retainers. His son Naozumi (who succeeded him) abandoned Christianity following the policy of the shogunate, and changed his domain to Hyūga Nobeoka. A new feudal lord named Matsukura Shigemasa took over the land which had belonged to the Arima clan (present day Minami-Shimabara).
The following year, the Edo shogunate issued an edict restricting the number of castles a feudal lord was allowed to have to one. In Japanese history, this is known as the "one castle per province" policy (ikkoku ichijou rei). This meant that both Hara and Hinoe became abandoned.
It was once said that after the Arima clan had moved to Hyūga, the majority of Hara castle's stone walls were carried to Shimabara castle. However, excavations at Hara which began in 1992 revealed that its walls match the way they appear on maps from the time of the Amakusa-Shimabara rebellion. These walls show how it was possible for rebel forces to resist defeat for such a long time (around 3 months).