Designed by Francesco Olivierri in the Baroque style and completed in 1644, the synagogue is named for its donor, Izaak Jakubowicz (d. 1673), also called Isaac the Rich, a banker to King Ladislaus IV of Poland.

For several nights now I have been dreaming that in the Jewish town of Kazimierz there is hidden treasure in the oven of the home of the poor Jew Ayzik Jakubowicz.

'"[4] On 5 December 1939 the Gestapo came to the Kraków Judenrat building and ordered Maximilian Redlich, the Jewish official on duty that day, to burn the scrolls of the Torah.

After the war, the building was used by a sculpture and conservation atelier and then by a theatre company as workshop space and for the storage of props.

When the building was planned, the design was considered by some diocesan officials to be too beautiful for Jews to have, which led to delays in the synagogue’s construction.