Seokguram Grotto

A valuable archaeological find in Fly Cave (Slovene: Mušja jama) indicates the influence of Greek civilization, where a cave temple was located after the end of the Bronze Age and in the Iron Age (wiki)

Cave of the Apocalypse

Grotta dell'Angelo

Gellert Cave Chapel

King Chu Cavern / Mot Mai Pagoda

Khao Thamorrat Cave is adorned with ancient buddhas.

Bin, Maijishan, Kizil and more

Agia Solomoni

Shancai and Shangshancai cave temples

Emeishan's Jiulao Cave of Xianfeng Temple

Saint Michael's grotto at Monte Sant'Angelo: "The cave comprised two cavities separated by a rock partition: a smaller one (...), where the Archangel purportedly left his footprints and where, at a later date, an altar was erected, known as the altar of the "Footprints". The larger of the two caves (...) was home to the altar upon which Michael is said to have lain his cloak, and a pitcher holding miraculous water (...)." "At a later date, the rock partition dividing the two caverns was demolished, thus creating a single large space". (Nomination file, p. 212, 215)
See en.wikipedia.org

Dwellings include altars, sanctuaries

Struga