Many who attended the prayer service called for unity amid the controversy.
Ramadan is the Muslim religious observance when the faithful fast from sunrise until sunset for an entire month. Breaking the fast is celebrated with Eid-al-Fitr. In light of the controversies, local religious leaders of other faiths made a point to celebrate Eid.
Friday's prayers were for not only to end Ramadan but to pray for the victims of 9/11 as the high holy holiday fell on the eve of the anniversary of the attacks.
The local Islamic community invited those outside of the faith to celebrate Friday.
"Please remember that those that stand in opposition are in a minority in this country," said State Rep. Mike Madigan, House Speaker.
"We must live in peace with one another," said Jesse White, secretary of state.
Leaders in the faith community spoke at press conference following the Eid service. They are troubled by recent attacks on Islam and its holy book the Quran.
"The God of us all weeps when we act out of fear rather than love. Today on this holy day, we pray that love will prevail and open our hearts," said Rev. Arlene Christopherson, United Methodist Church, Northern Illinois.
"We stand here and are saying to everyone to my brother there in Florida, he's a preacher, I'm a preacher, man you're wrong. It's wrong what's happening right now," said Rev. Gregory Livingston, Rainbow PUSH Coalition.
A minister in Florida had threatened to burn a Quran unless the proposal for an Islamic center and mosque is moved away from ground zero in New York.
Locally, Islamic leaders say the controversy is fueling misconceptions but the multi-faith gathering on Friday is an attempt to heal and unite all faith communities.
"Muslims are part of the American fabric, dream and future. Let us work together as citizens on the values engraved in our constitution," said Imam Kifah Mustapha, Mosque Foundation.
"I grieve because I know the pain you are experiencing and because of the shame I feel when some of my fellow Christian and some of our fellow US Americans turn their backs so willfully and blindly on our deepest help values," said Scott Alexander, Catholic Theological Union.
"There could have not been a better gift than you standing with us and supporting us," said Oussama Jammal, Mosque Foundation.
Rev. Livingston represented Rainbow PUSH at the press conference. He says Rev. Jesse Jackson is reaching out to the Florida minister in an effort to promote religious harmony.