The main hall is built on the top of a massive bedrock composed of wollastonite (the Ishiyama-dera Temple wollastonite) designated as a national monument from which Ishiyama-dera Temple derived its name (and, in addition, the Ishiyama-dera Temple wollastonite has been selected as one of Japan's 100 Geographical Conditions).
本堂は国指定天然記念物の珪灰石（「石山寺硅灰石」）という巨大な岩盤の上に建ち、これが寺名の由来ともなっている（石山寺珪灰石は日本の地質百選に選定）。