When Takauji ASHIKAGA deserted the Kenmu Government after suppressing the Nakasendai War in which Tokiyuki HOJO uprose in Shinano Province and temporarily occupied Kamakura, Nagatoshi battled against Takauji, supporting the court with Masashige KUSUNOKI and Yoshisada NITTA, but was defeated by Takauji who entered Kyoto after the Battle of Minatogawa in 1336, and was killed in the battlefield of Sanjo Inokuma.
足利尊氏が、信濃国で北条時行らが蜂起して鎌倉を一時占領した中先代の乱の討伐を契機に建武政権から離脱すると、楠木正成、新田義貞らと共に宮方として尊氏と戦うが、1336年（延元元年/建武3年）の湊川の戦いの後に京都に入った尊氏に敗れ、三条猪隈で討死する。