The Taiping Rebellion was one of the bloodiest chapters — if not the most — in human history. The movement leader was Hong Xiu-quan (洪秀全); he was an educated man but did not pass the Imperial Examinations. This failure led to emotional trauma and delirium where he dreamt of God declaring him to be a brother of Jesus Christ and instructing him to exterminate demonic spirits. He claimed to be the "Heavenly King" and preached that God asked him to build a utopian society that was devoid of the daily torments experienced by peasants at the time; he called this society the Kingdom of Heavenly Peace (太平天国).

Hong aimed at converting the entire Chinese population to his faith, a combination of Christianity and Chinese folk religion — the God Worshipping Society (拜上帝会).

The promise of a better life, such as collective property ownership, led millions of economically downtrodden peasants to follow his lead.

During its peak, the rebels controlled a large part of China, including the city of Nanjing, which was made their capital. The Taiping Rebellion lasted for 14 years, causing the death of 30 to 50 million people. In addition, much of the destroyed agricultural and industrial lands did not recover even by the beginning of the 20th century, directly contributing to the collapse of the Qing Dynasty.

The Jewish congregation was caught in the battles between the Taiping forces and the government army, who fought hard to prevent the rebels from advancing towards Beijing. The Jews were subjects of ruthless persecution by the Taiping army because they considered the Sect that Plucks the Sinews (挑筋教) a cult. As a result, many Jews concealed their identity and went into hiding; even more moved away and never returned.

Nanjing University’s Professor Xu Xin (徐新) conducted in-depth research into the nature and prominence of the Kaifeng Jewish community throughout history. He believes that their population ranged from a few hundred to a thousand or two during the community's early stages. Natural growth, immigration, and some conversion would then cause this number to grow. The Chinese-Hebrew Memorial Book (汉文-希伯来文谱牒) that was created after the 1642 flood recorded that the pre-flood Kaifeng Jewish population peaked at around four thousand and fell back below a thousand in 1642. It is likely that the community then regrew to about two to three thousand by the early 1700s; however, this would be short-lived, as even more floods, the Taiping Rebellion and other factors would cause a sharp decrease in numbers so that, by the turn of the century, the Kaifeng Jewish population would be under a thousand.

Between the visits of the two Chinese Delegates in 1851 and Reverend W.A.P. Martin in 1866, the Kaifeng synagogue collapsed.

For almost seven centuries, Kaifeng Jewish life revolved around the synagogue. Whenever the synagogue was damaged, the community had always rallied together, combined resources, restored the synagogue and preserved its contents. All four of the known stone inscriptions were dedicated to the rebuilding of the synagogue.

The synagogue was never rebuilt from this point forward, for the community no longer had the means. According to Zhao Ping-yu, a modern Kaifeng Jew who worked for the local Tax Bureau, the old synagogue collapsed before 1860, and the timbers were carted off and sold to a local mosque.

The 1663 Stone Inscription shared the same fate as the synagogue. It was last seen by the two Chinese Delegates in 1851 and could not be found when Reverent W.A.P. Martin visited the community in 1866.

The text of both sides of this tablet had been preserved in the Jesuit archives in Europe, as ink rubbings of the original.

In 1851, the Yellow River flooded again; hundreds of thousands of square miles of farmland were inundated, causing immense suffering and loss of life; millions were displaced, and famine was ubiquitous. This subsequently also deprived the Qing government of tax revenue in a time that it desperately needed money.

The Qing government, with reserves already depleted from the First Opium War (第一次鸦片战争, 1839-1842) and the Taiping Rebellion (太平天国之乱, 1850–1864), no longer had the financial means or expertise to provide effective disaster relief to those affected by the flood, resulting in the Nien Rebellion (1851–1868) — an armed uprising led by the poor peasants in northern China. Their slogan was “kill the rich and aid the poor.”

Even though the Nien Rebellion failed to topple the Qing Dynasty, it dealt a severe blow to the ruling regime, further depleting its resources and reducing public confidence in the government.

During the Yuan Dynasty, the Muslim community in China flourished. In their distrust of the Han Chinese, the Mongols appointed many Muslims to high-level government positions, and through them, the Han Chinese – third- and fourth-class citizens — were severely oppressed. This antagonism between the Hui Muslims and the Han Chinese seeped into the Qing Dynasty.

There were conflicts between the Han and Hui miners in Yunan as early as 1853. Significant tension also existed between the Hui and the Manchu officials in the region that by April 1856, 3,000 Muslims were slaughtered by the Qing authorities around the provincial capital of Kunming. This led to large waves of Muslim rebellions against the ruling regime.

The leader of the movement, Du Wenxiu (杜文秀, 1823–1872), was born to a Han Chinese family but converted to Islam. He blamed the tension between the Han and the Hui on Manchu policies and called for unity with the Han to kick out the Manchus. Du wore Chinese clothing but mandated the use of the Arabic language and kept halal.

With the help of French troops, the government crushed the rebellion. Remnant forces were severely prosecuted, and many fled to Burma and became known as the Panthay.

As the Muslim rebellions were brutally suppressed and the Chinese could not tell the difference between Jews and Muslims, the Kaifeng Jews naturally began to worry that they might soon face persecution — they, therefore, had to hide their Jewish identity to stay safe.

Professor Gao Wang-zhi (高望之, 1927–2009), a Chinese scholar of Semantics, addressed this point, "Because it was Qing policy to suppress the Hui (Chinese Muslim) harshly, and because the Jews lived in close proximity to the Hui, they were often looked down upon. Some felt compelled to conceal their identity and went as far as to obliterate their family names from those listed on the 1489 Stone Inscription. Racial oppression by the Qing government was the political cause of the disintegration of the Kaifeng Jewish community.”

The rebels of the Taiping Rebellion entered Kaifeng. To avoid the expected massacre, most of the city's residents fled, including the Jews — most never returned, further reducing the size of an already small population.

The Treaty of Tianjin is a series of documents signed in the June of 1858. It effectively ended the first phase of the Second Opium War (第二次鸦片战争, 1856–1860). The four western powers to sign the agreement were Russia, France, Great Britain, and the United States.

This was considered one of the "unequal treaties" by the Chinese.

In addition to the five Treaty Ports that opened up after the Treaty of Nanjing (南京条约, 1842): Guangzhou (广州), Xiamen (厦门), Fuzhou (福州), Ningbo (宁波) and Shanghai (上海), seven more cities were added to the list: Tainan (台南), Haikou (海口), Shantou (汕头), Haicheng (海城), Penglai (蓬莱), Danshui (淡水), Yantai (烟台), Yingkou (营口) and Nanjing (南京). A total of 23 foreign concessions were also set up.

The four nations of the Treaty were allowed to station diplomatic legations in Beijing, which was not a Treaty Port.

Anti-Christian sentiment in China started growing in the 1860s, after the Treaty of Tianjin and the Convention of Beijing, which lifted all restrictions on western missionaries' movement in the interior of China.

Chinese xenophobia culminated with the Tianjin Massacre of 1870. Before the incident, it was rumoured that French missionaries kidnapped or purchased Chinese children and “took out their eyes for medicine.” Subsequently, many French Catholic priests and nuns were killed.

To avoid war with the West, sixteen Chinese people were executed, and the Qing government issued an official apology letter.

The Boxer Rebellion between 1899 and 1901 marked the pinnacle of China's anti-West movement. This was an insurrectionist movement against the increased foreign intervention in China, including the work of the missionaries. The West called the insurgents boxers because many practised Chinese martial arts, the so-called boxing at the time. The boxers, allegedly convinced they were invulnerable to foreign weapons, upheld the slogan, "Support the Qing government and exterminate the foreigners."

The Boxer Rebellion was an anti-foreigner and anti-Christian uprising that started in northern China. The term Boxer was used because the rebels practised Chinese martial arts, which Westerners referred to as Chinese Boxing; interestingly, these Boxers believed they had Fist from God (神助拳) and were immune to the industrialised foreign weapons.

Towards the end of the 19th century, northern China suffered multiple natural disasters, from Yellow River floods to severe droughts. The privileges that the missionaries as well their Chinese converts had received after the Second Opium War (第二次鸦片战争, 1856–1860) — such as freedom to evangelise and build churches, which included converting Buddhist monasteries and Taoist Temples into Cathedrals — were not well received by the Chinese. They, in turn, used the foreigners as scapegoats for much of the social and economic turmoil caused by the disasters. The Boxers therefore rebelled and destroyed anything foreign, both property and people. They believed millions of soldiers would descend from Heaven to help them in their battle against foreigners. Their slogan was Support the Qing Government and exterminate the foreigners (扶清灭洋).

After a group of foreigners were trapped in the Beijing Legation Quarter (东交民巷) for 55 days, the Eight-Nation Alliance (八国联军) was formed to break the siege. The eight countries involved were the United States, Austria-Hungary, the United Kingdom, France, Germany, Italy, Russia and Japan. With the support of the Boxers, Empress Dowager Ci-xi (慈禧太后) declared war on the alliance.

China lost the war, resulting in the Boxer Protocol (辛丑条约) signed on 7th September 1901 where China agreed to execute officials who supported the uprising, allow foreign troops to be stationed in the capital, and pay 450 million taels in reparations, which was more than China's annual tax revenue.

According to Professor Xu Xin, during this period, anything foreign was actively sought after as targets of destruction; thus, "The Kaifeng Jews were frightened. To protect themselves from attack, they carefully and neatly chiselled their names off the memorial pillars that had stood in the synagogue compound for hundreds of years.”

The second half of the 19th century saw intense social and political upheavals, which had been very difficult for the small community of Kaifeng Jews. They scrapped their names off the stone inscriptions out of fear of persecution. They were to become even more impoverished and marginalised from this point forward.

Some scholars argued that Chinese tolerance for the Jews was what allowed them to stay as a distinct group for 700 years; others believed that it was this tolerance that contributed to their final disappearance — through assimilation. According to Professor Pollak, "The most clear-cut object lesson derived by historians and sociologists from the ultimate absorption of the Chinese Jews … has of course been that numerically small people transplanted into strange and enormously larger societies that do not grind them down or forcibly segregate them have little or no chance of retaining their own cultures or community integrity over the long run."

Professor Xu Xin, however, believes that the tolerance of Chinese society was not the driving force behind the final disappearance of this small colony; instead, it was the sequence of natural and political disasters that prompted their demise, including the Yellow River floods, droughts, diseases, the Taiping Rebellion, the Boxer Rebellion, the Muslim uprisings, and more. By the beginning of the 20th century, the Qing Dynasty had weakened to its core, and the Kaifeng Jews followed suit. Professor Xu argued that the Jewish congregation flourished as long as the Chinese empire was strong and stable and that the well-being of this small group of people correlated directly with the macro trajectory of the Great Qing.