It was damaged during the March 1920 massacre of the city's Armenians—and the destruction of their half of the city—by Azerbaijanis and experienced a decades-long decline well into the Soviet period.

In Azerbaijan, the cathedral is called "Gazanchy" (Azerbaijani: Qazançı) and the authorities have often denied its Armenian heritage, instead vaguely referring to it as "Christian"[6][7] or falsely labeling it a "Russian Orthodox" edifice.

The journalist Thomas de Waal notes that it was larger and more prosperous than either Baku or Yerevan, the current capitals of Azerbaijan and Armenia, respectively.

[19] According to Armenian political analyst Levon Melik-Shahnazaryan, the cathedral was set on fire three times between 1988 and 1991 using car tires.

[23] They reportedly sold off its bronze bell, which was later found in a market in Donetsk, Ukraine and was bought by an Armenian officer for three million rubles and returned to Armenia.

[28][29] Armenian volunteers, including noted activist Igor Muradyan, carried the wooden boxes of artillery and rocket shells out of the church immediately after the capture of the city.

[33] Restoration works were conducted by Volodya Babayan and primarily funded by Andreas Roubian, an Armenian evangelical benefactor from New Jersey, who provided $110,000.

[35] The first Divine Liturgy at the restored cathedral took place on July 19 with the attendance of Nagorno-Karabakh President Arkadi Ghukasyan and officials from Armenia.

"[39] On 16 October 2008, a mass wedding, sponsored by Levon Hayrapetyan [hy], a Russian-based businessman from Karabakh, took place in Nagorno-Karabakh.

[54] Human Rights Watch (HRW) noted that the two attacks "suggest that the church, a civilian object with cultural significance, was an intentional target despite the absence of evidence that it was used for military purposes.

On October 12 cellist Sevak Avanesyan played Krunuk (The Crane) by Komitas inside the partially ruined church.

[58] Armenia's Foreign Ministry issued an official statement describing it as "another crime of the military-political leadership of Azerbaijan... this action fully fits into its policy of Armenophobia developed for decades.

"[60] Armenia's first foreign minister Raffi Hovannisian wrote in the New York Post that for Armenians, "an attack like the one on the Holy Savior Cathedral isn’t just a matter of urgent current affairs.

[61] Azerbaijan's Defense Ministry officially denied it was behind the attack,[62] while its state news agency claimed the missiles came from the Armenian side.

[63] Azerbaijan's President Ilham Aliyev later stated: "We need to investigate this issue... We have doubts that could have been done by Armenians in order to blame us.

If it was done by Azerbaijani military units, that was a mistake, and we don’t have any historical or religious targets..."[64] In an interview with BBC, Aliyev stated: "the images of that church which I have seen, show that it is very minor damage.

[67] US Ambassador-at-Large for International Religious Freedom Sam Brownback stated on Twitter: "I am deeply saddened by the images of damage to the Holy Savior Cathedral (St. Ghazanchetsots).

A statement released by the International Association of Genocide Scholars (IAGS), signed by Israel Charny, Yair Auron, Matthias Bjørnlund, Tessa Hofmann and others argued that the strikes on the church are "a part of policy of the cultural genocide that the Azerbaijani government has been implementing over the past 30 years by systematically destroying the Armenian historical heritage.

"[71] In December 2020 Human Rights Watch's Europe and Central Asia director Hugh Williamson called on Azerbaijan to investigate the attacks.

"It has been over a month since Azerbaijan has retaken control of Shushi and the government needs to waste no time in investigating the attacks and holding those responsible to account.

[48] The town of Shusha was captured by Azerbaijani forces by November 9, 2020, when a trilateral armistice agreement was reached between Armenia, Azerbaijan and Russia.

[75] A report by Caucasian Knot quoted several Azerbaijani state officials who claimed that the renovation project aimed to restore the "original" appearance of the church, which, according to them, lacked the conical dome until it was added by the Armenians following Shushi's capture in 1992.

[10][74] In June 2023 Azerbaijani Ambassador to the Holy See Ilgar Mukhtarov stated that the church, "misappropriated by Armenians, is currently regaining its original appearance.

"[78] At a media forum in Shusha in July 2023, Aliyev stated: "We do not touch the historical heritage of the Armenian people.

[90] In 2001, the Shusha State Historical and Architectural Reserve, which includes Ghazanchetsots Cathedral,[1] was added to the Tentative List of UNESCO World Heritage Sites from Azerbaijan.