Under the Toyotomi government, the territory of the temple came to include the precincts of Hoko-ji Temple (Great Buddha) immediately to the north and Rengeo-in Temple, but Myoho-in Temple was highly regarded by the Tokugawa government and Hoju-ji Temple became treated as an 'inge' (branch temple that supports the main temple) of Myoho-in Monzeki Temple.
豊臣政権下では、すぐ北にあった方広寺(大仏)が法住寺や蓮華王院の寺域を包摂するということもあったが、徳川政権によって妙法院が重要視されるようになると、妙法院と一体視され、法住寺は妙法院門跡の｢院家｣として待遇された。