"For us Islam does not belong to Germany", the party's website reads.
Wagner had engaged in some anti-Muslim rhetoric himself before converting.
Kalbitz that Wagner had previously been active in the party's Christian wing. "Germany is mutating into a different country", he once said about Muslims emigrating to the nation. That regional committee occupies a particularly influential role; it is headed by Alexander Gauland, a major party figure who heads the AfD's delegation in Parliament. He was a member of the state committee with responsibility for churches and religious communities. "Only afterwards was it known that he had converted to Islam", Friese told media.
"The party has no problem with that", said AfD spokesman Daniel Friese in the eastern German state of Brandenburg.
The party, known by its German acronym AfD, has campaigned against what it considers the "Islamization" of Germany because of immigration and higher birth rates among the country's Muslim population.
Wagner, for his part, confirmed his resignation during an interview with the newspaper Der Tagesspiegel, saying that "it is a private matter". "We view this as his personal decision", Edler said.
The party said it stood for the constitutional right of religious freedom, regardless of Wagner's conversion. But he insisted that the AfD had not pressured him to leave its ranks.
The party touts an anti-immigration, anti-Islam platform. It has strongly criticised the German Government's decision to allow more than a million refugees into Germany in 2015. Its political manifesto also includes various anti-Islam references.
It argued that increasing the number of Muslims in the country was a danger to Germany's state, society and values.
As more German papers began to report about Wagner's conversion on Wednesday, the AfD's Brandenburg branch took to Facebook to respond to the rumors.
At the bottom of the post was an image. Some of the ads had a picture of a pig with the caption, "Islam?"