Swedish police on Sunday arrested 15 people who were trying to prevent Salwan Momika from burning a copy of the Muslim holy book.
The incident took place in Malmo's Varnhemstorget region, home to dense Muslim population.
Some 100 protesters threw stones and bottles at police and Momika, an Iraqi refugee living in Stockholm, after the anti-Islamic firebrand burned a copy of Quran under police protection.
Police moved away Momika from the scene following a brawl and arrested 15 protesters.
Large police presence continues in the area in case of an incident, said Malmo police.
Along with Denmark, Sweden has also met with wide-ranging criticism for permitting public desecration of the Quran under police protection.
Swedish-Danish politician Rasmus Paludan, the leader of the far-right Stram Kurs (Hard Line) Party, has burned copies of the Quran in the Swedish cities of Malmo, Norrkoping, Jonkoping, and Stockholm, including during Easter last year.
On June 21, he burned a copy of the Quran outside the Turkish Embassy in Sweden.
Momika made headlines a week later, when he burned a copy of the Quran outside a mosque in Stockholm during Eid al-Adha, one of the major Islamic religious festivals celebrated by Muslims worldwide.
On July 20, outside of the Iraqi Embassy in Sweden, he threw a copy of the Quran and the Iraqi flag on the ground and stomped on them, later burning a Quran copy outside of the Swedish parliament on July 31.
Iranian immigrant Bahrami Marjan held similar provocative acts in Angbybadet, an area near Stockholm, on Aug. 3.
Momika also staged another Quran burning outside the Iranian Embassy early in August, and another in front of the Stockholm Mosque last Thursday.
Though acknowledging that these acts hurt Sweden's image and put security at risk, Momika is still able to get permission from the authorities.
Swedish security services have also said the country's security situation has deteriorated after the ongoing Quran burnings.