Government-allied forces had engaged in torture, ethnic cleansing and widespread sexual violence, and have faced accusations of committing a genocide against Tigrayans. The Tigray Defense Forces (TDF) also engaged in the extrajudicial killings of civilians, war rape, using civilians as human shields, and widespread looting and destruction of civilian infrastructure in the Afar and Amhara Regions.

The EHRC claimed in November 2020 that the Mai Kadra massacre could constitute a crime against humanity. Human Rights Concern Eritrea claimed in February 2021 that crimes against humanity occurred during the war, in particular in the "appalling treatment of Eritrean refugees in the Shimelba and Hitsats camps" and called for an immediate independent international enquiry.

Many sources have accused the Ethiopian and Eritrean governments of engaging in crimes against humanity via ethnic cleansing of Tigrayans. In its 26 February 2021 report on the Axum massacre, Amnesty International described the indiscriminate shelling of Axum by the ENDF and EDF in January 2021 as possibly "amount[ing] to war crimes", and the following mass executions of Axum civilians by Eritrean troops as a crime against humanity.

War rape and sexual violence were widespread throughout the war, and was perpetrated by virtually all sides. According to one witness in May 2021, girls as young as 8 and women as old as 72 were among those being raped. Such sexual violence was often accompanied by other forms of physical and mental abuse. Physical abuses included burning their victims with hot iron or cigarettes, forcing metal rods or nails into their victim's genitals, etc. Mental abuses included raping their victim in front of their family members, forcing their victims to rape their family members, calling their victims derogatory words and ethnic slurs, etc. After being subjected to sexual violence, many women became infected with STIs like HIV, and often found difficulty seeking treatments due to a combination of shame and the collapse of medical infrastructure due to the war.

A UN investigation in September 2022 confirmed the reports of widespread rape and sexual violence by all parties, including the practice of mass rape as perceived retribution by the TDF, as well as the use of sexual slavery by Ethiopian and Eritrean forces.

Soldiers and militias often subjected Tigrayan women and girls (including pregnant women and young girls) to rape, gang rape, sexual slavery, sexual mutilation, and other forms of sexual torture. According to nine doctors in Ethiopia and one in a Sudanese refugee camp interviewed by CNN, sexual violence in the Tigray war violated laws regarding rape as a weapon of war. The women treated by the doctors stated that the ENDF, EDF and ASF soldiers who raped them described Tigrayans as having no history and culture, that the intent was to "ethnically cleans[e] Tigray", to "Amharise" them or remove their Tigrayan identity and "blood line." One of the doctors, Tedros Tefera, stated, "Practically this has been a genocide." In March 2021, The Daily Telegraph argued that testimonies supported the view that sexual violence was being weaponized, stating that "Survivors, doctors, aid workers and experts speaking to the Telegraph all pointed to rape being systematically used as a weapon of war by Ethiopian and Eritrean forces." Reasons for the rape that were stated to the victims included the aim of "cleansing Tigrayan blood." These reports of targeted, mass sexual violence against Tigrayans was corroborated by an April 2022 joint Human Rights Watch–Amnesty International report on the Western Zone, describing similar occurrences.

In January 2022, Amnesty International published a report stating that acts of rape and violence by the TPLF in the Amhara Region "may have been committed as part of a systematic attack against the Amhara civilian population." Survivors spoke of being gang raped, beaten and called ethnic slurs, often in front of their children. Reportedly, some TPLF fighters used the rape of Tigrayan women by pro-government forces as a justification for committing sexual violence themselves. In March 2022, the EHRC published a report stating that the TDF committed widespread and systematic acts of sexual violence against women and girls in the Afar and Amhara regions, including through gang rape and rape with foreign objects.

According to a report by The New York Times released in February 2021, confidential U.S. government documents described Amhara Region officials and armed forces as carrying out ethnic cleansing in the Western Zone, "deliberately and efficiently rendering Western Tigray ethnically homogeneous through the organized use of force and intimidation […] Whole villages were severely damaged or completely erased." Many Tigrayans fled across the border to Sudan, and those unable to flee were captured, and forcibly transferred to other parts of Tigray. In March, the United Nations Office for the Coordination of Humanitarian Affairs (OCHA) stated that "tens of thousands of people [had] been displaced from [the Western Zone] allegedly on ethnic grounds." The OCHA also confirmed that the zone was run by Amhara regional authorities, with humanitarian access "only [being] possible through Amhara Region." The Norwegian Refugee Council estimated that between 140,000 and 185,000 people had fled from the Western Zone to Shire, in the span of around 2 weeks in March 2021.

In contrast to towns with majority Tigrayan populations, the Times said that towns with majority Amhara populations were "thriving, with bustling shops, bars and restaurants."

In a 240-page report by Human Rights Watch and Amnesty International released on 6 April 2022, it was documented that Amhara Special Forces engaged in systemic campaigns deliberately targeting Tigrayans in the Western Zone. Tigrayans were often killed en masse, forcibly expelled, or otherwise experienced a number of crimes against humanity, including torture, rape, sex slavery, forced disappearances and arbitrary detention. In some cases, the Mai Kadra massacre was used as a justification to commit mass killings in "revenge", while in other cases, there was "little apparent motive beyond spreading terror." According to one witness, recounting what she discovered upon returning to her hometown in December 2020:

In Dansha, I saw the heads of people who had been beheaded around the gates of my home. The people say that Tigrayans' dead bodies shouldn't go to the grave.... The smell of dead bodies. I saw bodies where limbs were separating itself from each other because they had been left out for too long.

Tigrayans had their personal documents either confiscated or destroyed, and while the new Western Zone authorities issued new ID cards, they were reportedly not given to Tigrayans. The aforementioned IDs were required to access any essential service in the area, and when one resident attempted to get one, an administrator allegedly told him that orders "from above" were made to not give them to Tigrayans.

Tigrayans were also told, in no uncertain terms, to leave the Western Zone or be killed; some recalled seeing pamphlets telling them to leave within 24 or 72 hours if they did not want to die. 42 Tigrayans who were interviewed by Reuters gave broadly similar accounts of receiving papers explicitly mentioning this, with some of them also saying that they witnessed Tigrayans being rounded up by "Amhara gunmen." At the same time, federal Ethiopian and Amhara forces prevented civilians from trying to cross the border into Sudan, telling them to go back to their homes "in an apparent attempt to present a veneer of normalcy."

Both Amhara and federal Ethiopian authorities had repeatedly denied that ethnic cleansing or targeted ethnic violence was taking place in the area. Prime Minister Abiy dismissed reports of crimes committed by the ASF, saying in an April 2021 speech to Ethiopian parliament that "portraying [the Amhara Special Forces] as a looter and conqueror is very wrong." The Ministry of Foreign Affairs said Ethiopia "vehemently opposes such accusations," describing them as "completely unfounded," "spurious" and "[blown] out of proportion."

Yabsira Eshetie, the administrator of the occupied Western Zone, claimed that "no one was kicking them out, no one was destroying their houses even. […] It is lawful here", and said that "only criminals had been detained." Gizachew Muluneh, head of Amhara Regional Communication Affairs, denied the reports of ethnic cleansing in the Western Zone, calling it "propaganda", and claiming that the number of displaced Tigrayans was exaggerated. Gizachew also said, in response to U.S. criticism, that "these areas are not Tigrayan areas, [historically]. […] Our forces are not in the Tigrayan areas, rather our forces are in Amhara", making an apparent revanchist claim that the Western Zone belongs to the Amhara Region.

The BBC reported on 7 May 2022 that, according to the testimonies of 15 eyewitnesses, the ASF and Fano militias – throughout the occupied Western Zone – began systemically digging up mass graves of ethnic Tigrayans, burning their bodies, and moving them to another, separate location. Witnesses stated that this started to occur a few days after funding for a UN war crimes investigation into the Tigray war was approved in March 2022 (which Ethiopia voted against). This practice is alleged to have occurred Humera, Adebay and Beaker.

Charges of forced removals of Tigrayans continued into late 2022, even as peace agreements were being signed and implemented by the federal government and the TPLF. On 10 November, according to an aid group (which chose to remain anonymous), over 2,800 people (including children) were held in detention centres for at least a year, before Fano militias rounded them up into trucks and moved them to a town near Sheraro in the North Western Zone, which lies outside of Amhara's territorial claims.

Human Rights Watch and Amnesty International described Tigrayans being targeted with impunity, both by military and civilian groups:

Federal and allied forces looted Tigrayan homes, businesses, livestock, and crops as they took over towns and villages. Amhara Special Forces, Fano militias, and Eritrean military forces […] carried out the bulk of the looting, but groups in civilian clothes, some armed, others not, later joined them. […] Two interviewees said they saw security force members loot homes and businesses, selectively targeting Tigrayan property.

Anti-Tigrayan forces engaged in what HRW and Amnesty described as "pillag[ing]", with "schools, courts, churches, and health centers", in addition to civilian houses, being subject to looting. Amhara and Eritrean forces also took harvests, livestock and medicine from Tigrayan farmers, who were threatened with violence if they did not comply; these actions caused the looted areas to face "extreme starvation" by June 2021. Multiple witnesses, from separate villages, gave similar descriptions of Amhara militias and security forces "waiting for farmers to collect or harvest [sorghum crops] before stealing [them]." The new government of the occupied Western Zone did little to help the local Tigrayan population, and in a number of cases, actively participated in marginalizing and discriminating against them. The HRW–Amnesty report described them as "complicit in the theft of Tigrayan property". The authorities placed restrictions on their ability to harvest food, and denied them access to international aid.

A witness to the Axum massacre stated that the EDF "burned crops […] forced farmers and priests to slaughter their own animals […] stole medicine from health facilities and destroyed the infrastructure." Reports of Eritrean looting continued into late 2022, with allegations that the EDF was seizing food and other materials from Tigrayan homes, in violation of the November 2022 peace agreement.

Mark Lowcock, who formerly led OCHA, stated in October 2021 that the Ethiopian federal government was deliberately starving Tigray, "running a sophisticated campaign to stop aid getting in" and that there was "not just an attempt to starve six million people but an attempt to cover up what's going on." Ethiopian troops had reportedly withheld food from going to Tigrayan civilians who were suspected of having links to Tigrayan fighters. A student based in Europe, and in contact with her family in Tigray Region, said that in the Irob woreda where her family lives, "If you don't bring your father, your brothers, you don't get the aid, you'll starve." De Waal argued that the looting by the EDF of cars, generators, food stores, cattle, sheep and goats in the Tigray Region was a violation of international criminal law that "prohibits a belligerent from removing, destroying or rendering useless objects indispensable to the survival of the civilian population" (Rome Statute, Article 7, 2.(b)).

In early April 2021, the World Peace Foundation argued that Article 8(2)(b)(xxv) of the Rome Statute of the International Criminal Court was likely to be relevant to the case of starvation in the Tigray war. The authors concluded that the Ethiopian and Eritrean governments were responsible for starvation, listing evidence in Section 4 of their report. The authors argued that "circumstantial evidence suggest[ed] that [the starvation was] intentional, systematic and widespread." Additionally, a September 2022 UN commission concluded that the Ethiopian government, along with forces allied with them, engaged in deliberate efforts to deny the Tigray Region "access to basic services […] and humanitarian assistance," leaving 90% of Tigrayan residents in dire conditions. The commission also stated that they had "reasonable grounds to believe" that the Ethiopian government was using deliberate starvation as a war tactic, and called on both the federal government and the TPLF to let these services resume without hindrance.

In June 2023, the Lowenstein Human Rights Clinic of Yale Law School, in a summary of its 18-month study mostly based on public reports, stated that the Ethiopian federal government and its allies had extensively looted and attacked and blocked supplies of food, water, healthcare, electricity, cash, fuel, and humanitarian relief in Tigray during the war. The report stated that they were using starvation as a method of combat, in violation of international humanitarian law, and called for investigations to determine if these actions constituted war crimes, crimes against humanity or genocide.

A March 2022 Ethiopian Human Rights Commission (EHRC) report stated that the TDF "carried out widespread and organized pillaging, looting and destruction" of civilian infrastructure in the Amhara and Afar Regions, including government offices, businesses, schools and healthcare facilities; 2,409 health facilities were destroyed or damaged; a total of 4,310 schools damaged, of which 1,090 were "completely destroyed". The report concluded that the conduct of the TDF was the biggest cause of forced displacement in Amhara and Afar.

Analysis of satellite imagery, done by UK-based researchers at DX Open Network, confirmed that Tigrayan forces burned a farming village to the ground near the town of Agamsa in Kobo district, Amhara Region; according to the researchers, the village in question did not appear to be used for military purposes. A report by The Telegraph characterized these actions as "war crimes".

There have been several reported attacks on humanitarian workers, including attacks by Ethiopian government soldiers. The Danish Refugee Council and the International Rescue Committee reported killings of their staff in early December 2020. Although the Ethiopian federal government claimed to have given "full and unhindered access for humanitarian actors to operate in all parts of the [Tigray] region," many humanitarian agencies reported having been repulsed at army checkpoints and blocked from entry to various regions. There were accusations by US officials that armed forces were specifically singling out humanitarian workers for an attack. Violence against healthcare workers and the destruction of health facilities is a violation of international laws regarding medical neutrality, and has been described as such in regards to the Tigray war.

On 23 March 2021, a driver from Médecins Sans Frontières was beaten by Ethiopian soldiers after witnessing extrajudicial killings by Ethiopian government soldiers. Following the 23 June bombing of Togoga, there were reports of Ethiopian government soldiers firing on ambulances to prevent them from reaching the injured. On 25 June 2021, three MSF workers were found murdered near their car in Tigray.

In early February 2021, a writer for Ethiopia Insight, who had spent two months walking between villages in central Tigray, described scenes of towns and cities being completely abandoned, and that "once the center of trade, exchange and hope", they had turned into "the scene of war crimes that [can] never be fully articulated".

Extrajudicial executions of civilians by the ENDF and EDF were reported in and around Adigrat, Hagere Selam, Hitsats, Humera, Irob, Axum, Chefa Robit, and Amuru, among others.

Witnesses and survivors, including refugees in Sudan, reported that the Eritrean Defence Forces carried out a massacre in Axum that killed between 100 and 800 civilians in late November 2020. These reports have been corroborated by a number of news agencies and human rights organizations. The Eritrean government denied these allegations, and expressed anger at Amnesty International's report on the massacre, claiming it was "transparently unprofessional" and "politically motivated," accusing Amnesty of fabricating evidence.

A witness to the first part of the Axum massacre stated that the EDF soldiers had been ordered to kill all Tigrayan males older than four years old. Alem Berhe, who was in Mekelle on 3 November, on the evening of which the Northern Command attacks occurred, escaped to Addis Ababa after two months. Alem stated that the EDF's orders were "to exterminate you [Tigrayans] – all of you" above the age of seven years. Another witness described the limit as either "any male over the age of 14" or "those who 'pee against the wall.'"

In February 2021, footage surfaced on the internet showing what appeared to be the aftermath of a massacre, roughly geolocated near the Debre Abbay monastery. The videos (dated 5 January 2021) featured multiple people wearing Ethiopian army uniforms and speaking Amharic, with one noted as saying "you should have finished off the survivors." The video's authenticity was verified by multiple news outlets as genuine, with total estimates of dead civilians ranging from between 30 and 40. The Daily Telegraph described the full video as "too graphic to publish."

In early March 2021 (and again in June that same year), graphic video clips surfaced of a massacre taking place in Mahbere Dego, Tigray. Soldiers in ENDF uniforms were recorded rounding up a group of unarmed men in civilian clothing, "shooting them at point-blank range", and tossing their bodies off of a nearby cliff. Investigations by CNN World and BBC Africa Eye (in collaboration with Bellingcat and Newsy) judged the footage to be authentic.

Amharic-language conversations can be heard in the footage, with one voice saying "I wish we could pour gas over them and burn them"; another voice can be heard saying "This is the end of woyane […] we don't show mercy."

In early September 2021, the Tigray Defense Forces were accused of extrajudicially killing 120–200 villagers in Chenna Teklehaymanot and 600 residents of Kobo district in the Amhara Region. In both incidents, residents said that Tigrayan forces had killed villagers who had resisted looting. On 9 December 2021, Human Rights Watch published a report in which residents described witnessing Tigrayan forces summarily execute dozens of civilians in the village of Chenna and the town of Kobo between 31 August and 9 September 2021.