16th–18th centuries 
In terms of religion, Protestant ideas first appeared in the middle of the 16th century. During Gáspár Heltai‘s service as preacher, Lutheranism grew in importance, as did the Swiss doctrine of Calvinism. By 1571, the Turda (Torda) Diet had adopted a more radical religion, Ferenc Dávid‘s Unitarianism, characterised by the free interpretation of the Bible and denial of the dogma of the Trinity. Stephen Báthory founded a Catholic Jesuit academy in Klausenburg in order to promote an anti-Reform movement; however, it did not have much success. For a year, in 1600–1601, Cluj became part of the personal union of Michael the Brave. Under the Treaty of Carlowitz in 1699, Klausenburg became part of the Habsburg Monarchy.
In the 17th century, Cluj suffered from great calamities, suffering from epidemics of the plague and devastating fires. The end of this century brought the end of Turkish sovereignty, but found the city bereft of much of its wealth, municipal freedom, cultural centrality, political significance and even population. It gradually regained its important position within Transylvania as the headquarters of the Gubernium and the Diets between 1719 and 1732, and again from 1790 until the revolution of 1848, when the Gubernium moved to Hermannstadt (now Sibiu). In 1791, a group of Romanian intellectuals drew up a petition, known as Supplex Libellus Valachorum, which was sent to the Emperor in Vienna. The petition demanded the equality of the Romanian nation in Transylvania in respect to the other nations (Saxon and Hungarian) governed by the Unio Trium Nationum, but it was rejected by the Cluj Diet.
19th century 
Beginning in 1830, the city became the centre of the Hungarian national movement within the principality. This erupted with the Hungarian Revolution of 1848. At one point, the Austrians were gaining control of Transylvania, trapping the Hungarians between two flanks. But, the Hungarian army, headed by the Polish general Józef Bem, launched an offensive in Transylvania, recapturing Klausenburg by Christmas 1848. After the 1848 revolution, an absolutist regime was established, followed by a liberal regime that came to power in 1860. In this latter period, the government granted equal rights to the ethnic Romanians, but only briefly. In 1865, the Diet in Cluj abolished the laws voted in Sibiu, and proclaimed the 1848 Law concerning the Union of Transylvania with Hungary. Before 1918, the city’s only Romanian-language schools were two church-run elementary schools, and the first printed Romanian periodical did not appear until 1903.
After the Austro-Hungarian Compromise of 1867, Klausenburg and all of Transylvania were again integrated into the Kingdom of Hungary. During this time, Kolozsvár was among the largest and most important cities of the kingdom and was the seat of Kolozs County. Ethnic Romanians in Transylvania suffered oppression and persecution. Their grievances found expression in the Transylvanian Memorandum, a petition sent in 1892 by the political leaders of Transylvania’s Romanians to the Austro-Hungarian Emperor-King Franz Joseph. It asked for equal rights with the Hungarians and demanded an end to persecutions and attempts at Magyarisation. The Emperor forwarded the memorandum to Budapest—the Hungarian capital. The authors, among them Ioan Raţiu and Iuliu Coroianu, were arrested, tried and sentenced to prison for “high treason” in Kolozsvár/Cluj in May 1894. During the trial, approximately 20,000 people who had come to Cluj demonstrated on the streets of the city in support of the defendants. A year later, the King gave them pardon upon the advice of his Hungarian prime minister, Dezső Bánffy. In 1897, the Hungarian government decided that only Hungarian place names should be used and prohibited the use of the German or Romanian versions of the city’s name on official government documents.[