The final flight from South Africa touched down in Lagos today and brought 308 more citizens back to Nigeria.
Officials organized the airlift after attacks broke out in April.
President Bola Tinubu directed the Ministry of Foreign Affairs to help citizens leave.
As a result, teams arranged several flights from Johannesburg.
The process went beyond an initial June 30 deadline so everyone who wanted to return could board.
In total, more than 1,500 Nigerians came home through this effort.
Minister of State for Foreign Affairs Bianca Odumegwu-Ojukwu welcomed the group at the airport.
She noted the operation saved lives and thanked the diplomats and airline crew who managed the flights.
This marks the end of the evacuation effort as relations between the countries remain tense.
Nigerian officials say they continue to monitor the situation for any citizens who stayed behind.
