In a release Thursday, the university said it reconsidered the plan. It says Muslims will instead gather on the quadrangle before heading into a room in the chapel for their weekly prayer service.
Duke spokesman Michael Schoenfeld says the previous plan to use the chapel tower didn't have the intended effect of helping to unify people on campus.
Under the canceled plan, members of the school's Muslim Students Association would have recited the call lasting about three minutes from the bell tower.
The plan drew the ire of evangelist Franklin Graham, son of the Rev. Billy Graham and leader of the Samaritan's Purse charity, who urged Duke alumni to withhold support because of violence against Christians that he attributed to Muslims.
The private university in Durham, northwest of Raleigh, was founded by Methodists and Quakers, and its divinity school has historically been connected to the United Methodist Church. It has nearly 15,000 students, including about 6,500 undergraduates. The school's insignia features the Christian cross and a Latin motto translated as "learning and faith."
The university says it has more than 700 students who identify themselves as Muslim, and it hired its first full-time Muslim chaplain in 2009. Muslim students have been holding prayer services in the basement of the chapel for the past two years.