The Hunan Army, an unpaid and barely fed militia commissioned by the Qing Empire, lost all their discipline and committed mass-scale random murder, wartime rape, looting and arson against the civilians of Nanjing, seen as "rebels".

In June 1863 Qing Gen. Bao Chao took Jiufu Island (九洑洲) and the Taiping Army lost control of the entire northern shore of the Yangtze.

Imperial Gen. Bao Chao subsequently led his force across the river and camped on the southern bank outside the Shence (神策) Gate of Nanjing.

By mid-November regions including Chunhua (淳化), Jiexi (解溪), Longdu (龙都), Hushu, Sancha Town (三岔镇) had fallen under the Qing army's control.

Five days after the death of Hong Xiuquan on June 1, 1864, Li Xiucheng was finally put in charge of all military and political affairs, but it was already too late—the fate of the city and its defenders was sealed.

On July 3, Dibao Castle (地保城, nicknamed Dragon's Neck 龙脖子) on the Purple Mountain fell into the Qing army's hands.

The attackers divided into four fronts after entering Nanjing as previously planned: The street fights were fierce and bloody and the resistance was much tougher than expected.

The militia soldiers were unpaid and barely fed, and with this total victory in their final objective—after years of bitter campaign away from their families and their homes, [...] younger women were dragged off and the remaining able-bodied men were forced into service as porters to carry away huge loads of loot from the city—gold, silver, silks, furs, jade.

Even some of Zeng Guoquan’s own aides who entered the city to investigate the looting were robbed and beaten by roving gangs of Hunan soldiers.

On July 28, the overall commander of the battle, Zeng Guofan, reached Nanjing from Anqing and ordered Li to write his confession; he was executed after its completion on August 7.

Only Zun (遵) King Lai Wenguang succeeded in breaking out with his 3,000 cavalry to eventually join and lead the Nien Rebellion, during which he continued to fight for another four years.

The first Chinese indigenously built bolt-action single-shot rifle appeared in 1864, and although they were few in number, proved themselves over other firearms and certainly over ancient weapons such as swords, sabres, spears and lances.