Thereafter, on June 2, 1582 Mitsuhide AKECHI, who was his relative, staged the Honnoji Temple Incident, and Fujitaka himself was also asked to become involved in the incident, but he stuck to his position being anti-Mitsuhide and was approved as the main domain of Tango by Hideyoshi TOYOTOMI.
その後、天正10年(1582年)6月2日に親戚関係にあった明智光秀が本能寺の変を起こし、藤孝自身も加担するよう誘われるが、反光秀の立場を貫き、豊臣秀吉から丹後の本領を安堵されている。