The demonstration was held as 26 men were sent back to Afghanistan from Germany under a controversial deal between Kabul and the European Union.
The returnees are the second batch of failed asylum seekers deported over recent months after a mid-December charter flight returned 34 others from Germany.
The forced deportations prompted reactions from protestors, who staged a peaceful demonstration at the city’s airport on Monday night.
Protests were held at Frankfurt Airport on Monday night
Afghanistan is simply at war, which is why we are protesting
Sarmina Stuman of the Afghan Refugees Movements
About 250 activists arrived at the terminal holding banners as they chanted “no borders, no nation, stop deportation!”
One of the organisers, Sarmina Stuman of the Afghan Refugees Movements, told AFP: “Afghanistan is simply at war, which is why we are protesting against expulsions to a country like Afghanistan.”
The group of men left Frankfurt late on Monday night after being arrested earlier that day in raids carried out by German police.
Activists chanted "no borders, no nation, stop deportation!”
The would-be refugees consisted of convicted criminals and single men, who had been living mainly in Bavaria, Baden-Württemberg and North Rhine-Westphalia, according to reports.
A spokesman from Frankfurt Airport confirmed the group were escorted by 80 German police officers to their waiting plane.
They arrived safely back in the Afghan capital at about 07:30 on Tuesday.
About 250 are said to have taken part in the demonstration
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The deportation comes as Germany continues to deal with the large arrival of migrants in the country since 2015.
The country has been carrying out collective removals of illegal migrants based on an agreement reached by Brussels and Kabul in early October 2016.
Of the approximately 250,000 Afghans living in Germany, almost 12,000 have been ordered
The deportations have been criticised by some as large parts of the Afghanistan remains at risk of violence and is not on Germany’s official list of “safe countries of origin”.
Over a million migrants and refugees arrived in Germany since 2015, as Chancellor Angela Merkel urged the rest of Europe to do more to aid those fleeing war in the Middle East and Africa.