[7] Formed to counter Hindutva groups,[7] it was banned by the Indian Ministry of Home Affairs under Unlawful Activities (Prevention) Act (UAPA) on 28 September 2022 for a period of five years.

In 2012, the Government of Kerala claimed that the organization was a resurrection of the banned terrorist outfit Students Islamic Movement of India (SIMI), an affiliate of the Indian Mujahideen.

[27][28][29] The various allegations include connections with various Islamic terrorist groups,[30][31] possessing arms,[32][33][34] kidnapping, murder,[35][36] intimidation,[37] hate campaigns,[38] rioting,[39][40] Love Jihad[41] and various acts of religious extremism.

In 2010, the assault on Prof. T. J. Joseph who published a controversial question paper, supposedly insulting the Islamic prophet Muhammad, was linked to the PFI.

[52] On 6 July 2012, N. Sachin Gopal, a student of Modern ITC, Kannur and the district leader Akhil Bharatiya Vidyarthi Parishad, was allegedly stabbed by members of the CFI and PFI.

Investigations claimed that Ramalingam was murdered as part of a conspiracy after he tried to interfere in the conversions led by the Dawah team of PFI.

[44][45] Retired Indian army officer P. C. Katoch has claimed that the PFI maintains links with the Pakistani intelligence agency, ISI.

[63][64] In 2012, the Government of Kerala informed the High Court of their opinion that the activities of the PFI are inimical to the safety of the country and that it is "nothing but a resurrection of the banned outfit Students Islamic Movement of India (SIMI) in another form", in its argument to ban the organisation's Independence Day programme, dubbed "Freedom Parade".

[15][16][17] In July 2010, the Kerala Police seized country-made bombs, weapons, CDs and several documents containing Taliban and Al-Qaeda propaganda, from PFI activists.

[68] As of 6 September 2010, as informed to the state high court by the Kerala government, no evidence has been found by the police in its probe into the allegation of links to Hizbul Mujahideen, Lashkar-e Taiba (Let) or Al-Qaeda.

[71] In November 2017, Kerala Police identified 6 members of PFI who had joined the Islamic State, possibly by moving to Syria using fake passports.

[72] In November 2019, the Central Government provided Z category security to Justice S. Abdul Nazeer, one of the judges of the Supreme Court of India and part of the bench which passed the Ayodhya verdict, due to threats by the PFI.

[77] Two boys were kidnapped on 8 June 2011 from SBRR Mahajana College premises in Mysore and murdered by members of Karnataka Forum for Dignity (KFD), who sought ransom of 5 crore rupees to raise funds for their organisation.

[79] After the Assam riots in 2012, an SMS hate campaign was launched in the South of India threatening people from the North-East with retribution, particularly after Ramzan.

Investigators traced the source of these hate messages to Harkat-ul-Jihad al-Islami (HuJI) and the PFI, along with its affiliate organisations Manita Neeti Pasarai and Karnataka Forum for Dignity.

[82] At the time of the attack, Joseph was coming back from his duties at a private Christian college in Muvattapuzha and had been accused of blasphemy.

[95][96] On 1 January 2020 Union law minister Ravi Shankar Prasad stated that PFI may have played a part in violence surrounding some protests against the Citizenship (Amendment) Act (CAA).

[97][98][99] The Enforcement Directorate also informed the Ministry of Home Affairs and is investigating a Prevention of Money Laundering Act probe.

[107] In 2012, PFI launched a nationwide campaign "Why the Popular Front", detailing the alleged false accusations and attempts by mainstream media and other organisations to tarnish its image.

[112] The public meeting on 17 February 2009 which marked the conclusion of National Political Conference saw the merger of social organisations in eight states into the PFI.

[118] The Intelligence wing of Kerala Police had informed the High Court that PFI is the new face of banned Islamist group Students Islamic Movement of India (SIMI) and is engaged in fundamentalist and anti-national activities.

[121] The conference was addressed by Syed Shahabuddin, a former MP and Mulayam Singh Yadav, the Samajwadi Party leader, and Thol.

The key address of the conference was to plea the UPA government to implement the findings of Sachar Committee Report and the Ranganath Misra Commission.

[123] Following which, in May 2013, the organisation conducted a statewide campaign in Kerala, it started on 8 May from Kasargod and how the UAPA is being misused, and how they believe it is terrorising citizens who resisted oppression from a ruling elite.

[124][125] KM Shareef, the National General Secretary of PFI has asserted that reservation is the most immediate need of Muslims, referencing a report submitted by the Prime Minister's High Level Committee (Justice Rajindar Sachchar Committee) in November 2006, which identified the Muslim community as more backward than any other, and claimed that insufficient discussion on this topic was taking place in assemblies and parliament.

[130] In 2015, the PFI protested against the death sentence given to a democratically elected leader and Islamist affiliated with the Muslim Brotherhood,[131] Mohamed Morsi and his followers.

On 28 September 2022, the Government of India declared PFI as "unlawful association" and temporarily banned the organisation for five years under the UAPA act.