The main wave of Crimean Tatar repatriation occurred in the late 1980s and early 1990s when over 200,000 Crimean Tatars left Central Asia to return to Crimea whence they had been deported in 1944. While the Soviet government attempted to stifle mass return efforts for decades by denying them residence permits in Crimea or even recognition as a distinct ethnic group, activists continued to petition for the right of return. Eventually a series of commissions were created to publicly evaluate the prospects of allowing return, the first being the notorious Gromyko commission that lasted from 1987 to 1988 that issued declaring that "there was no basis" to allow exiled Crimean Tatars to return en masse to Crimea or restore the Crimean ASSR.

However, the government soon reconsidered its decision in light of the June 1989 pogroms against minorities in the Fergana valley where Crimean Tatars were exiled to, resulting in the formation of the Yanayev commission to readdress the possibility of allowing Crimean Tatars to return to Crimea. As result, on 14 November 1989, the Supreme Soviet issued a statement unequivocally condemning the deportation and exile of Crimean Tatars, re-recognizing them as a distinct ethnic group, and calling for the implementation of a state-sponsored repatriation of exiled Crimean Tatars to Crimea. Subsequently a commission led by Vitaly Doguzhiyev was formed to develop plans to carry out the repatriation and assist Crimean Tatars in returning to Crimea.

However, many of the state-sponsored return efforts did not last long due to the subsequent dissolution of the Soviet Union, and when the Crimean ASSR was re-established in 1991 it was designed as a regional autonomy, not as the de facto Crimean Tatar titular republic of the original Crimean ASSR. What followed was the mass return of a large portion of the Crimean Tatar diaspora in Central Asia, with an estimated 166,000 making it to Crimea by the end of 1991. Eventually over 200,000 Crimean Tatars returned, but many struggled to get suitable housing and citizenship in newly independent Ukraine for several years and to this day remain poorly integrated in Russian-dominated Crimean society. Today they compose an estimated 12% of the population of Crimea, living mostly in the central parts of the peninsula with negligible representation in the southern coastal regions where they were a majority before the deportation, which are currently very expensive to live in.

Ever since the deportation of 1944, Crimean Tatar exiles sought to return to their homeland. However, while most deported peoples, including the Chechens, Ingush, Kalmyks, were all allowed to return to their homelands, had their titular national republics restored, and were recognized as distinct ethnic groups. However, the same 1956 decree that restored the rights and republics of those deported peoples delimited Crimean Tatars, failing to recognize that they never part of the Volga Tatar people, and rationalized that the Crimean ASSR didn't need to be restored since the Tatar ASSR already existed, suggesting that "people of Tatar nationality formerly living in the Crimea" "return" to Tatarstan. Although Crimean Tatar rights activists attempted to explain to the Kremlin that they were a distinct ethnic group and not part of the Volga Tatar people colloquially simply called "Tatars", and only wanted to return to Crimea, they remained unrecognized, continuing to be counted simply as "Tatars" in censuses, and their repeated petitions requesting right of return to Crimea and restoration of the Crimean ASSR were rejected.

Eventually in September 1967 a carefully worded decree proclaiming that "Citizens of Tatar nationality previously living in the Crimea" were officially rehabilitated, leading to confusion among many Crimean Tatars about their status, but the subsequent fine print declared that they were "firmly rooted" in "places of residence" and reinforced that they could move about "in accordance with the passport regime". The initial vagueness of the announcements resulted in the first wave of Crimean Tatar returnees arriving in Crimea. While some of them were granted the required propiska (residence permit) to live in Crimea legally, many others were turned away and re-deported to Central Asia. The "lottery for the homeland" died off, with the number of Crimean Tatar families permitted to return to Crimea each year turning into a trickle by the 70's. Nevertheless, numerous Crimean Tatar families continued to seek repatriation to Crimea, only for most of them to be re-deported to Central Asia after being denied the required residence permit. Meanwhile, slavic settlers in Crimea from the mainland Ukraine and the RSFSR continued to flow into Crimea, and faced no barriers to obtaining housing and the required residence permit.

After decades of petitioning and delegations in 1987 Crimean Tatar activists organized a protest in the centre of Moscow near the Kremlin, which led the Soviet government to form a commission to evaluate the possibility of allowing Crimean Tatars to return to Crimea. The ensuing commission led by the hardliner Andrei Gromyko, who did not hide his disdain for Crimean Tatars and was reluctant to even meet with them, contained no Crimean Tatars on the board, and in July 1988 a formal conclusion statement was issued saying that there was "no basis" to allow mass repatriation of Crimean Tatars to Crimea and or the restoration of the Crimean ASSR on practical grounds due to the sharp demographic changes in Crimea over the decades, reaffirming the status quo of only seldom allowing small numbers of Crimean Tatars into Crimea on an individual basis.

In June 1989, Uzbek nationalist mobs attacked en masse the Meskhetian Turk minority (another ethnic group exiled in the Uzbek SSR) and other minorities to a lesser extent, including the Crimean Tatars. Earlier in December 1988 there had been a rally in Tashkent where Uzbek nationalists held banners saying "Russians - go to Russia! Crimean Tatars - go to Crimea!" Anecdotal evidence suggests that while approximately three-fourths of Crimean Tatars wanted to return to Crimea before the pogroms, almost all Crimean Tatars wanted to leave the Uzbek SSR afterwards, as they felt that the writing was on the wall that they would be the next target and the authorities would not be able to protect them when targeted by Uzbek mobs, just like they were unable to protect the Meskhetian Turks. In addition, the blatant violence against minorities in the riots limited the government's ability to claim Crimean Tatars and other exiled minorities had "taken root" in the Uzbek SSR or had no reason to want to leave.

After the Gromyko commission and the Fergana pogroms, the government decided to officially reconsider the possibility of allowing Crimean Tatars to return to Crimea. The Commission on the Problems of the Crimean Tatars headed by Gennady Yanayev was formed on 12 July 1989. Just like in the previous commission, members of the commission travelled across the Soviet Union to speak with Crimean Tatar diaspora communities in Central Asia as well as the leadership of Crimea and the Central Asia republics, as well as activists from across the spectrum of the Crimean Tatar rights movement ranging from the NDKT to the OKND. The conclusions, issued on 28 November 1989, cleared the way for the rehabilitation of the Crimean Tatar people and supported allowing their return to Crimea.