The ceremony to pass on the skulls and bones of the Herero and Nama peoples will take place at a church in Berlin at 08:30 GMT (10:30 local time).
This will be the third repatriation of human remains to Namibia – previous ones took place in 2011 and 2014.
The remains had been sent to Germany for use in now-discredited experiments, designed to prove the racial superiority of white Europeans.
Some 100,000 people are believed to have been killed as Germany crushed an uprising, beginning in 1904.
Despite admitting the massacres were genocide Germany has yet to fulfil a promise to give an official apology.
In January 2017, representatives of the Herero and Nama peoples filed a class-action lawsuit against Germany in New York to seek reparations. The judge has yet to rule on whether to hear the case.
Unlike with the victims of World War Two atrocities, Germany has also refused to pay reparations to victims, saying it pays millions of dollars of development aid to the country instead.