Zulfikarpašić returned to Bosnia and Herzegovina and in the lead up to the Bosnian War, as Bosnia and Herzegovina held an independence referendum for independence, he stood alongside the future Bosnian president, Alija Izetbegović. He was a member of Izetbegovic's Party of Democratic Action, but soon formed another party because of differing political views, the Muslim Bosniak Organization with Muhamed Filipović.