The temple came under the umbrella of To-ji Temple in 1879, and Daigo-ji Temple and Sanbo-in had their names on the lists of Jogaku-ji (a limited number of private temples protected by officials) and main head temples, but they became independent and publicly declared the Daigo School of the Shingon Sect in 1905.
1879年（明治12年）、東寺の傘下に入り、定額寺・大本山として、醍醐寺・三宝院がともに列したが、1905年（明治38年）には独立して、真言宗醍醐派を公称した。