Later, Muromachi dono Palace was repeatedly rebuilt, although on a smaller scale, but it went completely out of use when the 13th Shogun Yoshiteru ASHIKAGA constructed Nijo gosho Palace in 1559 in the grounds where the residence of the Shiba Buei family, which was one of Sankanrei ke (three families in the post of kanrei, or shogunal deputy), and moved there.
その後、室町殿は何度か小規模なものであるが再建が繰り返されたが、13代将軍足利義輝が1559年に三管領家の斯波武衛家邸宅跡に二条御所を造営・移転したために廃止された。