After the collapse of the Soviet Union and the independence of Turkmenistan, the migration of both Azerbaijanis and non-Turkmen to the outside of the country began.
During the "Turkmenization" policy in Turkmenistan, Azerbaijanis working in important jobs in the civil service lost their positions for various reasons.
During this period, a mass deportation of Azerbaijanis who allegedly did not have visas to stay in Turkmenistan was recorded in Turkmenbashi port.
After the death of Heydar Aliyev, on December 21, 2003, Azerbaijanis gathered at the Shia mosque in Turkmenbashi to celebrate his funeral.
At that time, the employees of the Ministry of National Security of Turkmenistan, who came to the mosque, demanded that the Azerbaijanis leave the place.