In the 1570s, Kuki allied himself with Oda Nobunaga, and commanded his fleet, supporting land-based attacks on the Ikkō-ikki. In 1574, his aided ensured a victory for Nobunaga in his third attempt to attack the Nagashima fortress. In 1576, he was defeated at Kizugawaguchi by the Mōri clan fleet, but 1578 brought victory in the second Battle of Kizugawaguchi, in which Kuki used 'iron ships' to repel the arrows and musket balls of the opposing Mōri clan's ships.
In 1587, he led Toyotomi Hideyoshi's fleet in a campaign in Kyūshū, alongside Konishi Yukinaga, Wakizaka Yasuharu and Katō Yoshiaki. Three years later, along with Wakizaka Yasuharu and Kato Yoshiaki he went on to lead the Siege of Odawara and the Siege of Shimoda. He continued in his role as commander of Hideyoshi's fleet, launching an invasion of Korea in 1592 from his flagship Nipponmaru.
In the Battle of Sekigahara, Kuki Yoshitaka fought alongside the Toyotomi forces, while his son Kuki Moritaka joined the opposing force, under Tokugawa Ieyasu. Following Tokugawa's victory, his son successfully guaranteed Yoshitaka's safety from Ieyasu. In a turn of fate, Yoshitaka committed seppuku before the news reached him.
- Ron, Roy (1999–2004). 'Genbukan Tokyo Shibu: Kuki Yoshitaka'. Ninpo.org Accessed 28 Dec 2004. Kuki Yoshitaka page.
- Turnbull, Stephen (1998). 'The Samurai Sourcebook'. London: Cassell & Co.