The chartered flight landed at 7am (02:30 GMT), airport officials in Kabul said early on Wednesday.
It marked the 35th deportation flight from Germany to Afghanistan since December 2016, DPA news agency reported.
A total of 963 failed asylum seekers have been sent back to Afghanistan since then. The last deportation flight from Germany was in December.
Other European countries have also resumed deportation flights.
The deportations have been deeply controversial, with critics saying the war-torn country is too dangerous to send asylum seekers back to. Almost daily attacks by the Taliban armed group are taking a toll on the civilians in the country.
Despite the start of peace talks in Qatar, the conflict between the Taliban and the Afghan government continues and the security situation is deteriorating. Afghanistan has been the scene of regular clashes and targeted killings across much of the country lately, and bomb and rocket attacks now occur almost daily in the capital Kabul.
In addition, the coronavirus pandemic has further worsened the living condition in the country. The United Nations warns that five million more Afghans will be in need of help this year due to the pandemic and conflict.
Source: Al Jazeera