In his later years, it is said he wished the Daikaku-ji Imperial line to be unified after the enthronement of Emperor Gonijoin's eldest son (his own child), Imperial Prince Kuniyoshi, however Emperor Godaigo did not like to be in power temporarily, and the relationship between him and his father, Emperor Godaigo, gradually became fragile, as the result, it is presumed the cloistered government was stopped and the Emperor started the directly ruled government, but there is another theory that retired Emperor Gouda stopped his cloistered government by his own will, and more study is needed to determine the truth of the matter.
晩年は後二条天皇の長子（自らの嫡孫）である皇太子邦良親王の即位によって大覚寺統が早期に一本化する事を望んでいたと言われ、中継ぎに甘んじない後醍醐天皇との父子仲は次第に疎遠になっていき、その結果院政停止・天皇親政に至ったと推測されているが、院政停止は後宇多院自身の希望ともいわれ、なお考証を要する。