Toyotomi Hideyoshi earnestly desired a child and visited Yoshino Mikumari Shrine (popularly known as Komori-no-Miya) to pray for one. He was subsequently blessed with the birth of Toyotomi Hideyori with his concubine Yodo-dono, and he is said to have been deeply grateful for the shrine's divine grace. Hideyoshi also held a celebrated cherry-blossom viewing at Yoshino in 1594, forging a lasting bond with this sacred mountain.

Toyotomi Hideyori (1593–1615) held deep reverence for Yoshino Mikumari Shrine, which was connected to his father Hideyoshi's prayer for an heir. In 1605, when Hideyori was just twelve, he donated funds to reconstruct the current shrine buildings. Completed with the support of his mother Yodo-dono and the Toyotomi retainers, these structures are designated Important Cultural Properties. The magnificent Momoyama-style halls harmonize with the cherry blossoms of Yoshino Mountain and preserve the cultural legacy of the Toyotomi house. Until Hideyori's death in the Summer Siege of Osaka (1615), Yoshino Mikumari remained a sacred site of special significance to the Toyotomi family.