By 1941, the Jews accounted for a quarter of the population of Tripoli and maintained 44 synagogues. In 1942 the Germans occupied the Jewish quarter of Benghazi, plundered shops, and deported more than 2,000 Jews across the desert, where more than one-fifth of them perished. Many Jews from Tripoli were also sent to forced labor camps. Conditions did not greatly improve following the liberation. During the British occupation, there was a series of pogroms, the worst of which, in 1945, resulted in the deaths of more than 100 Jews in Tripoli and other towns and the destruction of five synagogues.

A growing sense of insecurity, coupled with the establishment of the State of Israel, led many Jews to leave the country. Although emigration was illegal, more than 3,000 Jews succeeded in leaving, and many went to Israel. When the British legalized emigration in 1949, more than 30,000 Jews fled Libya.

At the time of Colonel Qaddafi's coup in 1969, some 500 Jews remained in Libya. Qaddafi subsequently confiscated all Jewish property and cancelled all debts owed to Jews. By 1974 there were no more than 20 Jews, and it is believed that the Jewish presence has passed out of existence.