Amnesty International stated that both Azerbaijani and Armenian forces committed war crimes during Second Nagorno-Karabakh War, and called on the governments of Armenia and Azerbaijan to immediately conduct independent, impartial investigations, identify all those responsible, and bring them to justice. UN Secretary-General António Guterres stated that "indiscriminate attacks on populated areas anywhere, including in Stepanakert, Ganja and other localities in and around the immediate Nagorno-Karabakh zone of conflict, were totally unacceptable". Columbia University's Institute for the Study of Human Rights recognized that violent conflict affected all sides in the conflict but distinguished "the collateral damage of Azerbaijanis" from "the policy of atrocities such as mutilations and beheadings committed by Azerbaijani forces and their proxies in Artsakh." Azerbaijan started an investigation on war crimes by Azerbaijani servicemen in November and as of 14 December 2020, has arrested four of its servicemen.

Armenian war crimes

Armenia shelled several Azerbaijani cities outside of the conflict zone, most frequently Tartar, Beylagan and Barda. Artillery strikes reported by Azerbaijani authorities included an attack on Beylagan on 4 October, killing two civilians and injuring 2 others, Goranboy on 8 October killing a civilian, Hadrut on 10 October, seriously injuring a medical worker, Fuzuli on 20 October, resulting in one civilian death and six injuries, Tartar on 20 October, resulting in two civilian deaths and one civilian injury and Tartar on 10 November, resulting in one civilian injury. By 9 November, there had been more than 93 civilian deaths and 416 civilian injuries in areas of Azerbaijan outside of the war zone.

Human Rights Watch reported that on 27 September, the Armenian forces had launched an artillery attack on Qaşaltı of Goranboy District, killing five members of the Gurbanov family, and damaged several homes. Human Rights Watch examined the severely damaged house and found several munition remnants in the courtyard that were consistent with fragments of large-caliber artillery. It also reported that the Armenian forces struck Hacıməmmədli of Aghdam District on 1 October, in an agricultural area, at around 11:00, killing two civilians. HRW stated that they had found no evident military objectives during their visit to the village. HRW also reported that the Armenian forces had launched an artillery attack on 4 October in Tap Qaraqoyunlu of Goranboy District at about 16:30, wounding a civilian. Then, on 5 October, Human Rights Watch reported that the Armenian forces fired a munition that landed in a field about 500 meters from Babı of Fuzuli District. The Azerbaijani authorities stated that they had identified the munition as a Scud-B ballistic missile and measured the crater as 15 meters in diameter.

Armenian forces heavily shelled the district of Tartar during the war, starting from 28 September. The bombardment caused widespread destruction and many civilian deaths. Thousands of people became refugees, making the city of Tartar a ghost town, and fled to neighbouring cities such as Barda. The Azerbaijani authorities stated that the Armenian forces had fired 15,500 shells on the territory of Tartar District until 29 October, with over 2,000 shells being fired upon Tartar in some days. Official Azerbaijani figures show that over a thousand civilian objects, including schools, hospitals, and government buildings were either damaged or destroyed during the bombardment. Human Rights Watch confirmed many of the targeted attacks on civilians and civilian objects, such as kindergartens and hospitals, by the Armenian forces. It also stated that the Armenian military forces had carried out unlawfully indiscriminate rocket and missile strikes on the Azerbaijani territories, and that such indiscriminate attacks were war crimes. The constant bombardment of the city prompted Azerbaijani officials to label Tartar as the Stalingrad of Azerbaijan, and the President of Azerbaijan, Ilham Aliyev, accused Armenia of trying to turn Tartar to the next Aghdam, also referred to as the Hiroshima of the Caucasus by the locals. Turkey also condemned the Armenian shelling of a cemetery in Tartar during a funeral ceremony, which foreign journalists at scene and Human Rights Watch confirmed. On 29 October, the head of the Tartar District Executive Power, Mustagim Mammadov, stated that during the war, 17 civilians killed, and 61 people injured in Tartar District as a result of the bombardment in Tartar. According to him, in total, about 1,200 people suffered from the bombardment. The Azerbaijani authorities reported two more civilian injuries later on.

Between 4 and 17 October, four separate missile attacks on the city of Ganja killed 32 civilians, including a 13-year-old Russian citizen, and injured 125 with women and children among the victims. The attacks were condemned by the European Union, and Azerbaijani authorities accused the Armenian Armed Forces of "committing war crimes through the firing of ballistic missiles at civilian settlements", calling the third attack "an act of genocide". Armenia denied responsibility for the attacks. The Artsakh Defence Army confirmed responsibility for the first attack but denied targeting residential areas, claiming that it had fired at military targets, especially Ganja International Airport. Subsequently, both a correspondent reporting from the scene for a Russian media outlet and the airport director denied that the airport had been hit, while a BBC News journalist, Orla Guerin, visited the scene and found no evidence of any military target there.

On 15 October, the Armenian forces shelled a cemetery north of the city of Tartar during a funeral ceremony, killing 4 civilians and injuring 4 more. This was confirmed by local journalists, TV Rain, and the Human Rights Watch. The Presidential Administration of Azerbaijan also confirmed that the cemetery was shelled in the morning.

On 25 October, a video emerged online of an Armenian teenager in civilian clothing helping soldiers fire artillery on Azerbaijani positions. Azerbaijan subsequently accused Armenia of using child soldiers. One day later, the Artsakh ombudsman released a statement claiming that the boy in the video was 16, was not directly engaged in military actions and was working with his father.

The Human Rights Watch reported that on 28 October, at about 17:00, the Armenian forces fired a munition on Tap Qaraqoyunlu of Goranboy District that produced fragmentation and killed a civilian.

The Artsakh Defence Army hit the Azerbaijani town of Barda with missiles twice on 27 and 28 October 2020, resulting in the deaths of 26 civilians and injuring over 83, making it the deadliest attack of the conflict. The casualties included a 39-year-old Red Crescent volunteer, while two other volunteers were injured. Civilian infrastructure and vehicles were extensively damaged. Armenia denied responsibility, but Amnesty International and Human Rights Watch stated that Armenia had fired, or intentionally supplied Artsakh with, the cluster munitions and Smerch rockets used in the attack. Artsakh acknowledged responsibility, but said it was targeting military facilities. Marie Struthers, Amnesty International's Regional Director for Eastern Europe and Central Asia, said that the "firing of cluster munitions into civilian areas is cruel and reckless, and causes untold death, injury and misery". The Azerbaijani ombudsman called the attack a "terrorist act against civilians". The use of cluster munitions was also reported by The New York Times. On 7 November, according to Human Rights Watch, the Armenian forces fired a rocket that struck an agricultural field near the village of Əyricə and killed a 16-year-old boy while he playing with other children. Azerbaijani authorities stated that they had identified the munition as a 9M528 Smerch rocket, which carries a warhead that produces blast and fragmentation effect. HRW reported that the researchers did not observe any military objectives in the area.

On 30 October 2020, Human Rights Watch reported that Armenia or Artsakh forces used cluster munition and stated that Armenia should immediately cease using cluster munitions or supplying them to Nagorno-Karabakh forces.

In mid-November, a video of a wounded Azerbaijani soldier Amin Musayev receiving first aid by Ukrainian journalist Alexander Kharchenko and Armenian soldiers after the ceasefire came into force was spread on social media platforms. Following this, a video was released showing Musayev being abused inside a vehicle. It is reported that he was lying on the ground in the car and asked: "where are we going?" In response, the alleged Armenian soldier said, "If you behave well, go home," and cursed, after which it became clear that the Azerbaijani soldier had been kicked. On 18 November, a representative of the International Committee of the Red Cross (ICRC) in Yerevan said that information about this person was "being investigated." The ICRC's representative in Yerevan, Zara Amatuni, declined to say whether she had any information about Musayev. The Artsakh ombudsman said he had no information about the Azerbaijani soldier, but that if he was injured, he was "probably in hospital in Armenia." The Azerbaijani Foreign Ministry said in a statement that the issue was being investigated and will be reported to the relevant international organisations. According to the ministry, "the information about the torture of prisoners is first checked for accuracy and brought to the attention of relevant international organizations." On 25 November, ICRC's representatives visited Musayev and Karimov in Yerevan. On 5 December, the family of Musayev was informed of his condition through ICRC. According to a reported copy of the letter sent by Musayev, he stated that his condition was well. Musayev was returned to Azerbaijan on 15 December as part of the POW exchange deal. Azerbaijan had officially accused the Armenian side of ill-treating the Azerbaijani POWs. Several Azerbaijani POWs, in interviews with the Azerbaijani media outlets, had stated that they were tortured by their Armenian captors until being transferred back to Azerbaijan. Dilgam Asgarov, a Russian citizen of Azerbaijani descent, who was detained by the Armenian-allied forces alongside Shahbaz Guliyev, an Azerbaijani citizen, in 2014, during an incident in Kalbajar, in an interview to Virtual Azərbaycan newspaper he gave after being released, also stated that the Armenian captors had tortured the Azerbaijani POWs.

On 10 December, Amnesty International released a report on videos depicting war crimes from both sides. In one of the videos, the Armenian soldiers were seen cutting the throat of an Azerbaijani captive. The captive appears to be lying on the ground, whilst gagged and bound when an Armenian soldier approaches him and sticks a knife into his throat. Independent pathological analysis confirmed that the wound sustained led to his death in minutes. Eleven other videos showed violations upon Azerbaijani captives by the Armenian army. In several videos, Armenian soldiers are seen cutting the ear off a dead Azerbaijani soldier, dragging a dead Azerbaijani soldier across the ground by a rope tied around his feet, and standing on the corpse of a dead Azerbaijani soldier.