The burning was carried out by pastor Wayne Sapp under the supervision of Terry Jones, who last September drew sweeping condemnation over his plan to ignite a pile of Qurans on the anniversary of September 11, 2001 attacks.
Sunday's event was presented as a trial of the book in which the Quran was found "guilty" and "executed."
The jury deliberated for about eight minutes. The book, which had been soaking for an hour in kerosene, was put in a metal tray in the center of the church, and Sapp started the fire with a barbecue lighter.
The book burned for around 10 minutes while some onlookers posed for photos.
Jones had drawn trenchant condemnation from many people, including US President Barack Obama, Secretary of State Hillary Clinton and Secretary of Defense Robert Gates, over his plan to burn the Muslim holy book in September.
He did not carry out his plan then and vowed he never would, saying he had made his point.
But this time, he said he had been "trying to give the Muslim world an opportunity to defend their book," but did not receive any answer.
He said he felt that he couldn't have a real trial without a real punishment.
The event was open to the public, but fewer than 30 people attended.
Life in the normally quiet city of Gainesville is centered around the University of Florida. And while there were public protests against Jones' 9/11 activities, this event was largely ignored.
Jadwiga Schatz, who came to show support for Jones, expressed concern that Islam was growing in Europe.
"These people, for me, are like monsters," she said. "I hate these people."
Jones said he considered this event a success.
"This is a once-in-a-lifetime experience," he said.
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I'm a citizen of Pakistan and i'm Christian. Im not happy to hear about this, but i was not happy when Muslims burn our Christians when they were sleeping, they burn them alive by no reason, they insecure us all the time. Where did that goes? why dont media speak for them? problems which our Christians are facing where are those? Just to secure themselves people are converting religion in Pakistan where does that goes? I hate what this Pastor did because in our Religion we forgive whoever do wrong to us. And we are forgiving for the last many years BUT if any of our Christian stand up for us, he's assasinated. Everyone over here who talks about this Pastor is Muslim or Hindu, i might be voluntarily taking this step and many of you will find it quite annoying but thats the reality. I was born in Pakistan and i love my country but what is going on? We are not one of them,why are we paying for their deeds? Due to this, reaction will be on us, Muslims Tanzeems will burn us alive that's insane please stop it we are not doing anything, we never burn a single page Of Quran and we never even have Quran in our homes how can we burn it? We Christians are not brutal please do not make us one of them!