Ishida Mitsunari had asked Fujitaka to join the Western Army, but Fujitaka refused due to one of Ishida's schemes which resulted in Gracia's and his granddaughter's death. As a general in the Eastern Army, he garrisoned Tanabe Castle with around 500 soldiers. When Tanabe Castle was besieged by the Western Army, the general commanding the siege had great respect for Fujitaka. Because of this, the attack lacked the usual spirit involved in a samurai siege: the attackers amused themselves by shooting the walls with cannons loaded only with gunpowder. Fujitaka laid down arms only after an imperial decree from Emperor Go-Yōzei. However, this was 19 days before Sekigahara, and neither he nor his attackers were able to join the battle.
Fujitaka was buried in Kyoto, but has a second grave in Kumamoto, where his grandson Tadatoshi ruled.