His greatest success came as a result of the 2008 elections, wherein he and the Free Voters won 10.8% of the vote, putting them past the threshold required by the Bavarian Parliament.

On 13 October 2012, he was symbolically nominated as the leading candidate of the Free Voters in Bavaria for the local state election.

However, following the successful lawsuits against the percentage hurdle,[7] in May 2014 the Free Voters for the first time sent an MEP to the EU Parliament, Ulrike Müller.

Aiwanger has been accused of lack of leadership by members of the Federal Executive of Free Voters, especially regarding alleged poor housekeeping of some national associations.

[15] In August 2023, the Süddeutsche Zeitung reported on a pamphlet with antisemitic contents that Aiwanger may have authored and distributed at his high school some 35 years ago as a 17-year-old.

[17] The Süddeutsche Zeitung drew some criticism for publishing the story, six weeks before the 2023 Bavarian state election, without conclusive evidence and without talking to Aiwanger before publication.

[18] Bavarian premier Markus Söder demanded that Aiwanger answer 25 questions on the matter, including whether Aiwainger had actively distributed the antisemitic pamphlet.

[29] From 17 until 30 July 2013, the Aiwanger and the Free Voters successfully campaigned for a referendum to abolish college tuition in Bavaria.

The referendum “No to school tuitions in Bavaria” (German: Nein zu Studiengebühren in Bayern) earned 14.3% of the 2013 vote.

[30] Under Aiwanger's leadership, the Free Voters have also successfully abolished taxes regarding road improvement contributions (German: Straßenausbaubeiträge, shortened to Strab).