The Afghan Conquest of Kunduz took place from May to June 1859. The conflict was between the Qunduz Khanate and the Emirate of Afghanistan. The conflict began after Mir Ataliq, the ruler of Qunduz, though nominally under Afghan rule, wished to remain under a degree of high autonomy. Mir Ataliq rejected many of the Afghan demands to re-enter their suzerainty, leading to Afghan forces under Afzal Khan to began mobilizing. The Afghans assembled their forces along the border of Qunduz, with an envoy delivering an ultimatum, which the Mir Ataliq did not respond to. This led to the Afghans invading in May 1859.
The Afghans defeated the armies of Mir Ataliq in battle, forcing his abdication as the Afghans closed in on his capital, with his brother-in-law negotiating a peace settlement that saw the Afghans annex the Qunduz Khanate. Badakhshan was also subjugated under Afghan rule during this conflict.
Background
Afzal Khan, the governor of Afghan Turkestan, held conflicting relations with Mir Ataliq, the ruler of the Qunduz Khanate, and had been sending letters to the government centered in Kabul to allow a campaign into Kunduz. In the spring of 1858, Afzal Khan sent an envoy to Mir Ataliq, requesting he read the Khutbah in the name of Dost Mohammad Khan, as well as admitting officers into the country to assess revenues for taxation. Due to the demands effectively stripping the independence of Qunduz, Mir Ataliq rejected the offer and sent one of his brothers as an envoy to Takhtapul, rejecting the demands and also sending a message that was a disguised threat.
The envoy sent, a brother of Mir Ataliq, also supported the idea of Afghan sovereignty, which enraged Mir Ataliq. After providing a false pretense of allowing him to safely return, The Qunduz cavalry pursued him and caught him in the region of Dasht-i-Abdan, where he was executed. Another brother of Mir Ataliq was also imprisoned by the Mir Ataliq. Following this, Mir Ataliq sent letters to the governors of Aqcha, Maimana, Andkhui, and Sheberghan, asking that they revolt against the Afghan government. However, this was intercepted by Afzal Khan, and immediately wrote to Dost Mohammad Khan, requesting aid to be sent to tame Qunduz. Reinforcements were sent under Azam Khan, Sharif Khan, and Shams al-Din Khan.
On 11 August, another brother, or son of the Mir Ataliq was sent as an envoy to Kabul. The envoy persisted in showing Mir Ataliq's loyalty to the Afghan government, but also said that if they were to be attacked, they would see assistance from across the Amu Darya, such as with Bukhara. Dost Mohammad utilized his sharp diplomacy to convince the envoy that the Afghan government had no plans to attack Kunduz, giving the campaign more time to prepare.
The Afghans and Mir Ataliq continued to build up for the inevitable military conflict, spending the winter in key preparation, while Bukhara funded Hukumat Khan, the ruler of Maimana, attempting to provoke a revolt in Afghan Turkestan. In early February 1859, Afghan mobilization and movements near the border made Mir Ataliq go in person to Bukhara, requesting their complete aid. Bukhara however, believing that diplomatic negotiation with the Afghans could still be pursued, refused joining the war. Mir Ataliq's travel to Bukhara now made it appear that he was declaring rebellion against the Afghan government, and he returned disappointed to Kunduz.
Afzal Khan, now aware of what happened, demanded that Mir Ataliq cede the territories of Dahan-I-Ghuri, Baghlan, and Ishkamish. This was the entirety of the southern realm of Qunduz, and the districts were the most fertile and populous of the state, which led to Mir Ataliq declining the offer.
Not long after his return Mir Ataliq's return to Qunduz, Hakim Khan, the deposed ruler of Sheberghan, amended ties with the Afghans and returned to Sheberghan, where he was reinstated as governor under Afghan paramountcy. Following this, Ghazanfar Khan, the ruler of Andkhui, also submitted to Afghan rule on 6 May 1859. Afzal Khan further strengthened his army with the submission of these states. As a result, Mir Ataliq sent an envoy to Afzal Khan, requesting a grace period to allow Mir Ataliq to consider the terms, which was granted, with a period of one month to consider the demands.
Mir Ataliq failed to reply as the grace period expired, which resulted in the Afghan army, led by Azam Khan, and supported by Abdur Rahman Khan, marching across the border with over 20,000 men, and 40 guns.
