In its early years, its leadership was composed of native German Jews, while most of the Jewish community in Germany was made up of Polish-born Jewish Holocaust survivors who had come to Germany as displaced persons, fleeing from the sporadically anti-semitic communist regime of Poland. Thus, the organization called itself "Central Council of Jews in Germany" rather than "Central Council of German Jews." Over time, the Polish-born Jews or their children acculturated to German society and became leaders of the Jewish community. By the late 1980s, the organization considered changing its name. Since the collapse of the communist regimes of eastern Europe, Germany has experienced a great influx of Russian and other Jews from the former Soviet Union. Although most of the Jews now living in Germany are recent immigrants, the organization is dominated by the so-called "German" Jews (who themselves are primarily descended from the Eastern European immigrants of the immediate postwar years).
At various times in its history, the organization has faced corruption scandals, most notably under the administration of Werner Nachmann, involving financial irregularities. After Nachmann's death, Heinz Galinski, the chairman of the West Berlin Jewish community for 43 years, assumed the leadership of the Zentralrat and brought it stability and respectability. Under Ignatz Bubis, the Zentralrat assumed a much greater profile in German public life, and the Jewish community's leadership felt increasingly confident weighing in on public debates concerning Holocaust memory and German identity. In more recent years, the division between more observant and more liberal Jews has strained the organization, which remains (or claims to be) the sole representative body of the Jewish community in Germany and which generally supports strict observance. In April 2004, open controversy erupted between the leader of the Zentralrat der Juden, Paul Spiegel, and the leader of the more liberal organisation Union progressiver Juden in Deutschland, Jan Mühlstein. The latter demanded equal financial support from the government for his organisation.