The conflict began after Mir Ataliq, the ruler of Kunduz, though nominally under Afghan rule, wished to remain under a degree of high autonomy.

After providing a false pretense of allowing him to safely return, The Kunduz cavalry pursued him and caught him in the region of Dasht-i-Abdan, where he was executed.

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.

In early February 1859, Afghan mobilization and movements near the border made Mir Ataliq go in person to Bukhara, requesting their complete aid.

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.

This was the entirety of the southern realm of Kunduz, and the districts were the most fertile and populous of the state, which led to Mir Ataliq declining the offer.

Abdur Rahman Khan, predicting an attack, selected 2,000 men from his best cavalry, alongside four battalions of infantrymen, and established them on a secret route to flank the Mir's forces when they engaged the Afghans.

Unaware of the true size of the Afghan army, Mir Ataliq retreated, believing the relief of the fort to be a lost cause.

[5][15] The following morning after the Mir Ataliq's defeat, Abdur Rahman patrolled the area with 2,000 men, and found a mobilizing force of 8,000 cavalry centered at Chashma-yi Shir.

The Afghans them began bombarding the fort with cannons, demoralizing and keeping them awake, making them exhausted and unprepared for a final assault.

Nasrullah Khan, the ruler of Bukhara, was also unable to provide assistance to Mir Ataliq, with his forces diverted to conflict with a rebellion that began in Hisar.

A contingent of 600 Uzbeks in the Afghan army were sent to Kunduz, taking control of the city, with Afzal Khan arriving not long after.

Mir Ataliq continued to rule the region under Afghan paramountcy, and upon his death in June 1865, the realm passed to his sons.

The Afghan governor of Badakhshan held direct control over Andarab, Khenjan, Doshi, Nahrin, Baghlan, and Dahan-I-Ghuri.