Fifteen madrassas are involved in the government-funded project, each of which will link with three primary schools to share ideas about teaching methods and understand more about how each other works.
If the project is successful it will be expanded to Manchester and then Leicester.
Mohammed Ali, chief executive of the Bradford-based QED project, welcomed the Department for Children, Schools and Families funding for the project but urged the government to do more.
"With the current climate and suspicion of Islam we need to make sure we make the most of madrassas to reassure people they are not a breeding ground for terrorists," he said.
The project currently has funding of £180,000 per year for three years, after which time Ali hopes Bradford Council will continue the project.
Tahir Alam, assistant secretary general for education at the Muslim Council of Britain welcomed the project: "By working closer with madrassas, schools can hopefully be persuaded that Islam is an asset for these children and can help them prepare to live their adult life," he said. "Islam is part of the solution and not part of the problem."
