From 1580 to 1588, the castle was greatly expanded and modernized with multiple concentric enclosures and numerous yagura watchtowers.

The Mōri and Kobayakawa eventually came into conflict with Oda Nobunaga, and subsequently with Toyotomi Hideyoshi.

In 1595, Kobayakawa Takakage turned his estates in Chikuzen to his adopted son Hideaki, and retired to Mihara Castle.

Contemporary drawings show three double-story interconnected yagura located on the base; however, one theory states that a three-story tower was relocated to Mihara Castle in 1615 from Tomojo Castle, after that fortification was destroyed in accordance with the shogunate's "One-Country One-Castle" decree.

After the 1600 Battle of Sekigahara, the new Tokugawa shogunate assigned Aki and Bingo Provinces to Fukushima Masanori.

After the Meiji Restoration, the castle grounds were secured by the government for the construction of the Japanese Imperial Navy Saikai Naval Base; however, this plan was canceled due to concerns about the sedimentation of the Nuta River.

Land reclamation, especially for the construction of Japan National Route 2 moved the castle further from the seashore.

With the expansion and elevation of Mihara Station for the Sanyo Shinkansen in 1975, the castle grounds were further divided.