While a vibrant Jewish center had continued to exist in the Galilee following the Jewish–Roman wars, its importance was reduced with increased Byzantine persecutions and the abolition of the Sanhedrin in the early 5th century. Jewish communities of the southern Levant under Byzantine rule fell into a final decline in the early 7th century. and with the Jewish revolt against Heraclius and Muslim conquest of Syria, the Jewish population had greatly reduced in numbers. In early Middle Ages, the Jewish communities of southern Bilad al-Sham (Eretz Yisrael), living under Muslim protection status, were dispersed among the key cities of the military districts of Jund Filastin and Jund al-Urdunn, with a number of poor Jewish villages existing in the Galilee and Judea. Despite temporary revival, the Arab Muslim civil wars of the 8th and 9th centuries drove many non-Muslims out of the country, with no evidence of mass conversions, except for Samaritans.
The Crusader period marked the most serious decline, lasting through the 12th century. Maimonides traveled from Spain to Morocco and Egypt, and stayed in the Holy Land, probably sometime between 1165 and 1167, before settling in Egypt. He had then become a personal physician of Saladin, escorting him throughout his war campaigns against the Kingdom of Jerusalem. Following the Crusaders' defeat and the conquest of Jerusalem, he urged Saladin to allow the resettlement of the Jews in the city, and several hundred of the long-existing Jewish community of Ashkelon resettled Jerusalem. Small Jewish communities were also existent at the time in Gaza and in desolate villages throughout upper and lower Galilee.
The immigration of a group of 300 Jews headed by the Tosafists from England and France in 1211 struggled very hard upon arrival in Eretz Israel, as they had no financial support and no prospect of making a living. The vast majority of the settlers were wiped out by the Crusaders, who arrived in 1219, and the few survivors were allowed to live only in Acre. Their descendants blended with the original Jewish residents, called Mustarabim or Maghrebim, but more precisely Mashriqes (Murishkes).
The Mamluk period (1260-1517) saw an increase in the Jewish population, especially in the Galilee, but the Black Death epidemics had cut the country's demographics by at least one-third. In 1260, Rabbi Yechiel of Paris arrived in Eretz Israel, at the time part of Mamluk Empire, along with his son and a large group of followers, settling in Acre. There he established the Talmudic academy Midrash haGadol d'Paris. He is believed to have died there between 1265 and 1268, and is buried near Haifa, at Mount Carmel. Nahmanides arrived in 1267 and settled in Acre as well.
In 1488, when Rabbi Ovadiya from Bertinoro arrived in the Mamluk domain of Syria and sent back letters regularly to his father in Italy, many in the diaspora came to regard living in Mamluk Syria as feasible.