When Emperor Godaigo passed away in 1339, Chikafusa became the de facto leader of the Southern Court, but when Chikafusa himself died in 1354, the Southern Court again fell into decline; having lost the internal power struggle within the Ashikaga shogunate, Kiyouji HOSOKAWA switched allegiance to Masanori KUSUNOKI and the Southern Court and together managed to briefly occupy Kyoto, but in 1367 they were defeated, and thereafter the Southern Court lost its large-scale military might, and even suffered the loss of Hiroyo OUCHI and Tokiuji YAMANA, who submitted to the shogunate during the rule of Shogun Yoshiakira ASHIKAGA.
1339年（延元4年/暦応2年）に後醍醐天皇が死去すると親房が南朝の指導的人物となるが、親房が1354年（正平9年/文和3年）に死去すると南朝はまた衰微し、幕府内での抗争で失脚した細川清氏が楠木正儀らと南朝に帰順して一時は京都を占拠するものの1367年（正平22年/貞治6年）に敗れ、以降は大規模な南朝の攻勢もなくなり、足利義詮時代には大内弘世や山名時氏なども帰服する。