The German national team midfielder scored both of Dortmund's goals in their 2-1 win over Elversberg on Saturday and celebrated by taking off an invisible crown and placing it on the grass.
The gesture is linked to the "Ballers in God" movement, which, according to an investigation by ARD, is accused of describing homosexuality as a sin and abortion as part of Satan's plan.
Dortmund's largest supporters' group does not approve of the celebration.
"Dortmund is not a club that judges people based on who they love, their gender identity, where they come from, what religion they have or whether they are religious. Dortmund is a club where people from all parts of society stand together," the group writes in a statement on its website.
Nmecha celebrated with the same gesture when he gave Germany the lead against Curaçao at this summer's World Cup.
Amid the debate over the celebration, Germany coach Jürgen Klopp has asked to meet with Nmecha, according to Kicker magazine. Nmecha is part of Germany's squad for the ongoing Nations League.
On Instagram, Nmecha describes the whole thing as a misunderstanding.
“My celebration is not meant to highlight myself or any organization. Instead, it is about laying down my ‘crown’ before the soon-to-return King and directing attention to Jesus, who is my hope and my strength. My message has never been about promoting intolerance, discrimination or hatred in any form,” he writes.
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