Before the construction of the first synagogue Jews had shared a place in a mosque with Muslims. This mosque was called the Magak-i attari, i.e. the "Mosque in pit". Some say that Jews and Muslims worshipped alongside each other in the same place at the same time. Other sources insist that Jews worshipped after Muslims. This perhaps explains the Bukharan Jewish custom of saying "Shalom Aleyhim" ("Peace be with you") after morning prayer. This custom is not found amongst European Jews.

Before the Arab conquest there was a bazaar on the site of the Magak-i Attari It was a market for idols, potions and spices - attar (perfumes) and other goods. Besides this, there was formerly a Temple of the Moon (Mokh) close to this place. Narshakhi named the mosque, which was built on the site of former temple, "magok", i.e. "in a pit", because even then half of it was concealed from view by the rising soil level.