Top candidate Maximilian Krah will sit as a political wild card in the European Parliament and not with the AFD party. The exclusion could open up the possibility for AFD to be readmitted to its party group.
Krah has been involved in several scandals during the election campaign, including one of his assistants being formally accused by German authorities of spying for China's intelligence service.
When Krah later made controversial comments about Nazi Germany, it led to AFD being expelled from the far-right ID group in the European Parliament on 23 May.
When AFD's newly elected EU parliamentarians met in Berlin on Monday morning, they decided to expel Krah from the party's delegation to the European Parliament. However, no decision has been made about his future in the party. The party also has no opportunity to prevent an elected candidate from taking their seat in parliament.
"I wish my newly elected parliamentary colleagues all the best in their efforts to rejoin the ID group without me," Maximilian Krah wrote on social media.
"I believe this is the wrong path to take and that it sends a devastating signal to our voters, especially the young voters."
AFD became the second-largest party in the European election in Germany with a total of 15 seats – including Krah.
Alternative for Germany (AFD) had been part of the far-right ID group in the European Parliament, along with the French National Rally and the Italian Lega, but was expelled as recently as May following criticism of top candidate Maximilian Krah.
Since Krah was expelled from AFD's parliamentary group, there is an opening for the party to return. If so, ID could grow to at least 73 seats in the newly elected parliament.
ID also hopes to attract other newly elected parties and is discussing cooperation with several parties that are currently part of the ECR party group.