The Ben Ezra Geniza was discovered in 1890, when the ceiling of the storeroom collapsed. Thereafter, many documents were stolen from their hiding place. In 1892, Jacob Saphir, a Jewish researcher, took several thousand documents away, and wrote a description of the storeroom, besides giving an idea of its contents. In 1894, documents dating back to the 11th and 12th centuries were removed. According to Serag, the mutual architectural influence of Jews, Muslims and Christians appears clearly in the Ben Ezra Synagogue.
Christian influence shows in the building style itself, which is reminiscent of a basilica.
The ceiling is supported by 12 marble columns. Motifs used in many churches, like vines, sheaves of wheat and olive branches are also in evidence. Islamic influence is even more evident on the carved wood and the two chandeliers, on one of which are engraved the names of the four Rightly-Guided Caliphs. On the other, the name of Sultan Qalawun is inscribed, also in Arabic. Jewish symbolic and decorative elements include the star of David and the menorah.