At the end of May, Germany and Niger reached an interim agreement allowing the German military to continue operating its airbase in the capital Niamey until the end of August.
But negotiations to extend that agreement broke down, notably because the base's personnel would no longer benefit from immunity from prosecution.
Senior German and Nigerien military officials read out joint statements announcing the completion of the withdrawal.
"This withdrawal does not mark the end of military cooperation between Niger and Germany, in fact the two sides are committed to maintaining military relations," they said.
Five cargo planes carrying 60 German troops and 146 tonnes of equipment landed at the Wunsdorf air base around 6:30 pm local time (1630 GMT), where they were met by state secretary for defence Nils Hilmer.
Germany had operated the base in Niger since February 2016 and it once housed some 3,200 personnel.
Niger has been run by a military government since a coup d'etat in July 2023 ousted president Mohamed Bazoum, who has been held as a prisoner ever since.
The regime has turned its back on other Western allies such as France and the United States to turn towards Russia and Iran.
A similar shift has taken place in neighbouring Mali and Burkina Faso, which are likewise ruled by military leaders and faced with violence from jihadist groups.
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