[2] After the expulsion of the Jews in 1492, the synagogue was seized by the authorities and converted into the Hospital Santo Quiteria for people suffering from rabies.

At this celebration, the first Jewish prayer service in 443 years, openly and with full knowledge of the authorities, was held at the synagogue.

Restrictions varied depending on the location of the synagogue and whether or not Jews enjoyed a privileged status in that community.

In April 1250, Innocent IV ordered the Bishop of Córdoba to take action against the Jews for building a synagogue of an unacceptable height.

Documents from his reign record resentment toward a prominent new congregational synagogue:[3] The Jews of Cordoba are rashly presuming to build a new synagogue of unnecessary height thereby scandalizing faithful Christians, wherefore ... we command [you] ... to enforce the authority of your office against the Jews in this regard....[4]The Córdoba Synagogue has a gate in the eastern wall that leads into a small courtyard that measures slightly more than twenty-five square meters (270 square feet).

The entrance to the synagogue, the facade, is located on the northern wall of the courtyard with three openings: a door and two windows on either side.

This entrance hall functioned both as a cloakroom and a place for the maskilta (water basin for ritual ablutions).

The prayer hall is the largest room in the synagogue, but even it is small in comparison to most buildings or homes of the period.

The location of the hekhal was based on directions given by Maimonides in his authoritative legal code, the Mishneh Torah.

And a bimah should be set up in the center of the house, to enable the reader of the Torah or one who admonishes the congregation, to go up to it so that everyone will be able to hear him...."[3] The ceiling of the synagogue is made of thin wooden panels above thick beams that hold the ceiling in order to hide the gabled tile roof.

The ceiling is angled upward in order to give the sanctuary a greater feeling of height common in the architecture of Spanish synagogues.

The inscriptions featured inside the synagogue are mostly from Psalms, other books of the Bible, and piyyutim (liturgical poetry).

"This minor sanctuary has been refurbished by Yitzhak Mahab son of the wealthy Ephraim in the Hebrew year 5075 (1315 C.E.)