The headstones were used as building materials around the city, including for Greek Orthodox churches, while the Aristotle University of Thessaloniki was built on the grounds.

[7] In 1937, the Jewish community agreed to cede 30,000 square metres (320,000 sq ft) along the western border next to the university in exchange for having the remainder preserved.

[10] On 17 October 1942, Vasilis Simonides, the governor-general of Macedonia told the Jewish community to move the graves to two new cemeteries on the outskirts of the city.

[11] The cemetery was partly destroyed in the first week of December 1942 in a process overseen by the chief engineer of Thessaloniki municipality, Athanassios Broikos, and involving five hundred workers.

[9][12] Jewish community leader Michael Molho believed that the Christians were eager to destroy the cemetery quickly because they wanted to complete it before Allied liberation of the area.

[9]According to historians Carla Hesse and Thomas Laqueur, "Nowhere else, in no other great city, did the imperatives of modernity and nation-building telescope so decisively with the crisis of occupation and genocide.

[18] After the war, people (including city officials) were still carrying away Jewish gravestones each day and regularly looting the cemetery in search of valuables.

[9][20] According to historian Rena Molho, "one can still find, as the writer has personally witnessed, Jewish tombs decorating children's playgrounds, bars, and restaurants in modern hotels in the summer resorts of the Chalkidiki".