The chartered flight landed at 7:48 am (0318 GMT). It is the 39th deportation flight from Germany to Afghanistan since December 2016, DPA reported.
Berlin has now returned a total of 1,077 failed asylum seekers to Afghanistan.
Deportation flights usually occur monthly, but there was none in May.
The German Interior Ministry said it was postponed because the Afghan authorities saw the need for increased security measures around May 1 - the date that the USA and other NATO countries officially began withdrawing their troops from Afghanistan.
The deportations have been deeply controversial, with critics saying the war-torn country is too dangerous to return asylum seekers to.
Almost daily attacks by Taliban militants are taking a toll on Afghan civilians. The Islamic State militia is also active in the country.
Despite on-and-off peace talks, the conflict between the Taliban and the Afghan government continues and the security situation is deteriorating.
The US-led withdrawal has left the country in a state of uncertainty.
Since the start of May, at least 11 districts have been captured by Taliban insurgents. Soldiers surrender or retreat, leaving equipment and ammunition behind.
Afghanistan is experiencing regular clashes and targeted killings across much of the country, with attacks now occurring almost daily in the capital Kabul.
The coronavirus pandemic has further worsened Afghans' living conditions. Recently the country registered a significant increase in new Covid-19 infections and record daily death figures.