The relations between these two communities were at first very tense, and often erupted into physical violence. Avraham Ibn Daud testifies to the excommunication of Karaites from the Mount of Olives during the Hosha`ana Raba festival (celebrated on the seventh day of Tabernacles), and a letter by Ben Meir describes the murder of Rabbi Musa at the hands of descendants of `Anan.

At the beginning of the eleventh century, the Karaites became dependent on their community in Cairo, which was very powerful in the Fatimid court, who recognized them as a separate community. At the same time, the gaon Solomon ben Judah, head of the Yeshiva of Eretz Israel, aspired to improve the Karaite-Rabbinite relationsdespitethe fierce opposition of his fellow leaders, including his own son. who continued the practice of excommunication against the Karaites. This situation led the Karaites to complain to the Fatimid authorities in Cairo, who, in turn, decreed the freedom of the sect to celebrate their own holidays according to their calendar and customs. This decree was not observed, and consequently three of the Rabbanite leaders were imprisoned in Damascus. The easing of the tension between the two parties is reflected in the Karaites' involvement in solving Rabbinite disputes, and in the fact that we hear of Rabbanites who spent the night in the Karaite quarter on their way to bury their dead outside the city wall.