The society at University College London (UCL) published an image on its Facebook page showing "Jesus and Mo" having a drink at a bar.
The atheist group was asked by the UCL union to remove it, but refused and started a petition defending its freedom of expression.
A student Muslim group began a counter-petition asking for its removal.
UCL's Atheist, Secularist and Humanist society said its president Robbie Yellon was stepping down to be replaced by former vice president Michael Thor.
De topman is dus afgeserveerd. Dat smaakt naar meer.
http://www.bbc.co.uk/news/uk-england-london-16615312The Ahmadiyya Muslim Youth Association is continuing with its protest against the image, saying it has wider implications.
Adam Walker, the association's national spokesperson, said the two student groups had worked well together in the past and said the offence was unnecessary.
"The principle is more important than who is being attacked - this time it is Muslims and Christians but in the future it could be atheists themselves.
"There is no need to print these things other than to cause offence and history has told us that these things cause offence."
He added: "I wouldn't say we're specifically pursuing UCL atheist society, it's more about the broader principle."