In 1360 the Jews were expelled from Hungary, and some of the Jews of Bratislava took refuge in Hainburg (Austria). They returned in 1367 and resumed possession of their homes. In 1371 the municipality introduced the Judenbuch regulating financial dealings between Jews and Christians. Isaac Tyrnau officiated as rabbi in Bratislava about 1410. In 1392 King Sigismund exempted Christians for a year from paying the interest on loans borrowed from Jews; in 1441 and 1450 all outstanding debts owed to Jews were canceled; and in 1475 Jews were forbidden to accept real estate as security. An attempt by many Jews to leave Bratislava in 1506 was prevented by Ladislas II who confiscated the property of those who had already left.

The Jews were expelled from Bratislava in the general expulsion from Hungary in 1526, although they apparently continued to live in several places, including the Schlossberg ("Castle Hill"), outside the municipal bounds. The first Jew subsequently to reside within them was Samuel Oppenheimer, who received permission to settle in a suburb in 1692. He was followed by other Jews and a synagogue was built in 1695, where the first known rabbi to officiate was Yom Tov Lipmann. In 1699 the Court Jew Simon Michael, who had settled there in 1693, was appointed head of the community; he built a bet midrash and acquired land for a cemetery. By 1709 there were 189 Jews living in Bratislava and 772 by 1736. The Jewish quarter in the Schlossberg remained outside the municipal jurisdiction. It later passed to the jurisdiction of the counts Palffy, who gave protection to the Jews living there. In 1714 they granted a charter of privileges to the 50 families living in its precincts and in Zuckermandel. The Jews in the Schlossberg resided in a single row of houses, but in 1776 the municipality permitted Jews to settle on land owned by the city opposite these houses and thus to constitute a "Jewish street." The Jews living on the Palffy side, however, enjoyed different rights from those under municipal jurisdiction, the former, for instance, being permitted to engage in crafts and all branches of commerce. They enjoyed freedom of religious worship. After the status of the community improved, the customary provision of geese to the Viennese court on St. Martin's Day, formerly an onerous tax, developed into a ceremony (performed until 1917). The Jews in Bratislava pioneered the textile trade in Hungary in the 18th century. Under the direction of Meir Halberstadt the yeshivah became an important center of Jewish learning, while the authority of Moses Sofer (d. 1839) made Bratislava a center of Orthodoxy for all parts of the Jewish world. During the reign of Maria Theresa (1740–80) the representatives of Hungarian Jewry used to meet in Bratislava to arrange the tax administration.

During the revolution of 1848, anti-Jewish riots broke out. The Jewish quarter was put under military protection and Jews living elsewhere had to retire within it. Jews volunteered to serve in the National Guard but were opposed by the general public. Further outbreaks of anti-Jewish violence followed the blood libel case in Tisza-Eszlar in 1882 and 1883. From 1898 tension mounted between the Orthodox and the pro-Reform members of the community. After 1869 the Orthodox, Neolog, and status-quo-ante factions in Bratislava organized separate congregations. The Orthodox provincial office (Landeskanzlei) later became notorious for its opposition to Zionism. Jewish institutions in Bratislava included religious schools, charitable organizations, and a Jewish hospital (founded in 1710). The Hungarian Zionist Organization was founded in Bratislava in 1902 and the World Mizrachi Organization in 1904, both on the initiative of Samuel Bettelheim.