In mid-2000, the Russian government transferred certain military responsibilities to pro-Russian Chechen forces. The military phase of operations was terminated in April 2002, and the coordination of the field operations was given first to the Federal Security Service and then to the Ministry of Internal Affairs in the summer of 2003.

By 2009, Russia had severely disabled the Chechen separatist movement and large-scale fighting ceased. Russian army and interior ministry troops ceased patrolling. Grozny underwent reconstruction efforts and much of the city and surrounding areas were rebuilt quickly. Sporadic violence continued throughout the North Caucasus; occasional bombings and ambushes targeting federal troops and forces of the regional governments in the area still occur.[32][33]

In April 2009, the government operation in Chechnya officially ended.[9] As the bulk of the army was withdrawn, the responsibility for dealing with the low-level insurgency was shouldered by the local police force. Three months later, the exiled leader of the separatist government, Akhmed Zakayev, called for a halt to armed resistance against the Chechen police force from August and said he hoped that "starting with this day Chechens will never shoot at each other".[34] This marked the complete end of the Chechen conflict.

The exact death toll of the conflict is unknown. Russian casualties are around 7,500 (official Russian casualty figures)[35] or about 14,000 according to the Committee of Soldiers' Mothers.[36] Unofficial sources estimate a range of 25,000 to 50,000 dead or missing, mostly Chechen civilians.[37]