In 1855 the Yellow River had changed its course, entering the sea once more at Tianjin, to the great loss of the regions of Hunan and Anhui. In these two central provinces the peasant rising of the so-called "Nian Rebellion" (c. 1853-68) had begun, but it only became formidable after 1855, owing to the increasing misery of the peasants. This purely peasant revolt was not suppressed by the Manchu government until 1868, after many collisions. Then, however, there began the so-called "Mohammedan risings".

An offshoot of the Buddhist-inspired White Lotus secret societies, the Nian were motley bands of peasants, army deserters, and salt smugglers who had fomented sporadic outbreaks since the first decade of the 19th century. Oppressed by famine resulting from flooding during the 1850s and stimulated by government preoccupation with the Taiping, several Nian bands formed a coalition under the leadership of Zhang Lexing in 1855 and began to expand rapidly. Numbering from 30,000 to 50,000 soldiers and organized into five armies, they began to conduct plundering raids into adjacent regions. In 1863 they received a setback when their citadel, Zhihe (now Guoyang, Anhui province), was captured and Zhang Lexing was killed. However, they soon reorganized, and in 1864 they were joined by those Taiping soldiers not defeated in the fall of the Taiping capital at Nanjing that same year. They began to adopt guerrilla hit-and-run tactics, using mobile mounted units to strike at the weak points of the Qing armies and then retreating into strategic hamlets. The government, by then free from problems with the Taiping, began to concentrate on the Nian and adopted a strategy of blockade. The rebels were gradually trapped and defeated.

Meanwhile, inaction toward nationalization of railway lines in both Hunan and Hubei were criticized by the local press. Confidence in the Qing government among the populace continued to deteriorate in response to the escalation of the railway crisis.