Economically, the Reformation era was a time of significant growth for the city, a development in which Jews participated actively, as goldsmiths, publishers, furriers and butchers especially. Culturally the sixteenth century was also something of a golden age for Jewish culture in Krakow, with local Talmudic scholars and the books produced on the printing presses of Menachim Meisler and others enjoying high international prestige. As a mark of their growing authority, rabbis and elders of the Krakow community were chosen to represent Malopolska on the Council of the Four Lands when it met for the first time in Lublin in 1581. The ghetto area was expanded in 1583, and again in 1603, attaining a considerable size which it retained for the next two centuries, with a fence and stone wall along ul. Jozefa separating it from the rest of Kazimierz.

Economically, the community's heyday came to a end with the Swedish invasions (known popularly as the "Swedish Deluge") of the mid- seventeenth century , when Charles X's troops occupied the city and systematically destroyed large parts of it. By 1657, the ghetto population of around 4500 had declined by two-thirds, many Jews having emigrated to other parts of the country, notably the new capital Warsaw, in search of better times. Throughout the eighteenth century , the age-old struggle for economic ascendancy between Jewish and Gentile merchants and craftspeople continued apace, as elsewhere, culminating in the issue of an edict severely curtailing Jews' economic freedoms and even, in 1776, an order for them to leave Kazimierz altogether. The Austrian occupation of Krakow in 1776 in the wake of the First Partition temporarily put a lid on local squabbling. The Austrians' initial move was to incorporate the whole of Krakow directly into Austrian territory, abolishing the separate judicial status of Kazimierz and all other outlying districts in the process.

Under the terms of a nineteenth-century statute promulgated in the wake of the establishment of the Free City of Krakow (1815-46), the ghetto was officially liquidated and the walls separating it torn down, with a direct view to encouraging assimilation among the Jewish population. Jews were now permitted to live anywhere in Kazimierz, and with special permits, duly granted to merchants and craftsmen, to reside throughout the city area. It was another almost fifty years, however, before they were granted the right to vote in elections to the Austro-Hungarian Diet, eventually also benefiting from the Habsburg declaration of equal rights for all Jewish subjects of the empire.

The latter part of the nineteenth century was marked by a fierce struggle for influence among rival sections of the Jewish community in Krakow. On one side stood the assimilationists, favouring progressive integration of Jewish culture, and in some radical instances, even religion, into mainstream Catholic society, often accompanied by a noticeable hint of Polish nationalism. On the other stood the ranks of conservative Orthodox Jewry, zealously committed to the preservation of a radically distinct way of life. In Krakow, as elsewhere, the European-wide upsurge in anti-Semitism in the closing years of the century led to a marked dampening of support for the assimilationist programme, a trend exacerbated by intensifying economic competition between Gentiles and Jews in which the latter generally appeared to come out best. The early twentieth century was also a period of growing political activity, with the formation of several Jewish political parties, notably the first Zionist groupings.

The period following the end of World War I and the regaining of national independence was one of intense population growth in Jewish Krakow, the community rising from 45,000 people in 1921 to nearly 57,000 a decade later, and over 64,000 on the eve of the Nazi invasion of Poland. Most, but by no means all, of Krakow's Jews lived in Kazimierz. The inward-looking and mostly poor Hassidim dominated the synagogues, prayer houses and Talmudic schools of the quarter, while the more integrated, upwardly mobile sections of the community moved out into other city districts, the Stare Miasto included, and increasingly adopted the manners and educational habits of their Gentile neighbours. This was a period of rich cultural activity, notably in the Jewish Theatre, established in 1926 in southern Kazimierz, the biggest star being the legendary Ida Kaminska, still remembered today as one of the great prewar Polish actresses. Contemporary accounts make it clear that Kazimierz possessed a memorable and unique atmosphere, the predominantly poor but intensely vibrant Jewish community carrying on unchanged the traditions of its forebears, seemingly oblivious to the increasingly menacing world outside it.

Following the Nazi invasion of Poland, Krakow was occupied by Wehrmacht units on September 6, 1939, and within days the Nazi Security Police issued an order directing all Jewish-owned commercial enterprises to be daubed with a Star of David. A month later, the General Government was established with its capital in Krakow, and the new Nazi governor Hans Frank arrived to take over. A series of increasingly restrictive laws began to affect Jews. From the end of November, 1939, all Jews were required to wear the notorious blue and white armbands, and in May 1940, Frank embarked on a drive to enforce this edict, a campaign that continued through the winter.

From here on the situation deteriorated. In March 1941, an official ghetto area was established. Located in the Podgorze district, south of Kazimierz across the river, the ghetto was surrounded and effectively sealed off by two-metre-high walls. Through the rest of the year an increasingly ruthless schema developed. Jews from the area surrounding Krakow were herded into the cramped and insanitary ghetto area, and from June 1942 onwards, fearsome and bloody mass deportations from the ghetto to Belzec concentration camp and eventually Auschwitz-Birkenau, began. Compounding the torture and destruction, a new forced labour camp was set up in November 1942 at Plaszow, just south of the ghetto.

In a final determined drive, a major SS operation on March 14, 1943 removed or murdered the remains of the ghetto population. Those not killed in cold blood on the streets were either marched out to Plaszow or transported to the gas chambers of Auschwitz. Thus was nearly seven hundred years of Jewish presence in Krakow uprooted and effectively destroyed. Under the ruthless rule of its notorious commander Amon Goeth , Plaszow was transformed into a murderous work camp where those who didn't die from hunger, disease and exhaustion were regularly finished off at whim by the twisted Goeth himself, who was later caught, tried and eventually executed in Krakow in September 1946. In January 1945, with Soviet forces rapidly advancing west, many of the surviving camp inmates were moved to Auschwitz (the workers at Oskar Schindler's factory excepted), and the site dynamited by the camp guards.

In many ways, the postwar history of Krakow's Jews parallels that of other Polish cities with notable prewar Jewish communities. By the end of 1945, roughly 6000 survivors had returned to the city, about a third of whom had lived there before the war. Subsequent waves of emigration to Israel and the USA went in step with the ups and downs of domestic and international politics, the largest occurring in the wake of the post-Stalinist "thaw" (1957), the Six Day War and the semi-official anti-Semitic campaigns subsequently unleashed in Poland in 1968-69, leaving an increasingly introverted and elderly community hanging on by the 1980s, mostly in Kazimierz. Developments since the communist demise of 1989 have been marked by a notable upsurge in interest in the city's Jewish past, symbolized by the increasingly popular annual summer Jewish Festival (June/July) held in Kazimierz, now into its tenth year, and a determined drive to renovate and rebuild the fading architectural glories of the quarter. The city's Jewish population can never be fully reconstituted, but the effort to ensure that their culture and memory receive due recognition today continues.