[5][6] Frustrated with the constraints they experienced while working for The Sun newspaper, Premesh and Gan decided to use the Multimedia Super Corridor (MSC) pledge to create a space for uncensored journalism.

It reported that Sin Chew Daily had doctored a photograph of Malaysia's ruling party to remove the image of former deputy prime minister Anwar Ibrahim, who then had recently been imprisoned for corruption.

[9][10] According to BBC News, the Malaysiakini report led to "worldwide infamy" for Sin Chew Daily, and the newspaper later issued a public apology.

[11][12] In April 2001, Malaysiakini made news again when it discovered and reported the secret detention of 10 political activists for participating in a rally in favour of the imprisoned Anwar Ibrahim.

[23] On 5 November 2016, right-wing Umno leader Jamal Yunos led a group of his Red Shirt protesters to the entrance of the news portal's new office premises in Petaling Jaya.

Asia Mobiliti, selected for the nine-month DRT trial in Selangor is co-owned by Ramachandran Muniandy, the husband of Youth and Sports Minister Hannah Yeoh, and ex-Malaysiakini CEO Premesh Chandran.

[25] Premesh, who was still a leading shareholder in Malaysiakini, dismissed allegations of nepotism and argued an open tender was unsuitable because there were only two companies with the necessary Apad registration to participate in Selangor’s proof of concept trial.

The ruling came amid concern among activists about freedom of expression in Malaysia, with Malaysiakini perceived to be particularly targeted as one of the most widely read independent news media source[citation needed].

[29] On 19 February 2021, Malaysiakini was found guilty of contempt by the Federal Court of Malaysia over five user comments posted on the website that the Malaysian Attorney General claimed undermined public confidence in the judiciary.

It quoted Gan as saying that the court's decision would "have a tremendous chilling impact on discussions of issues of public interest and it delivers a body blow to our continual campaign to fight corruption.

"[34] On 26 April 2017, Pasir Salak MP Tajuddin Abdul Rahman filed a defamation suit against Shah Alam MP Khalid Abdul Samad, Malaysiakini subsidiary KiniTV and the New Straits Times Press Bhd (NSTP) He claimed that Khalid had uttered defamatory statements laced with curse words at two media conferences held at the Parliament lobby in 2016.

[38] Through the years, Malaysiakini has won various awards and accolades from the International Press Institute, Reporters Sans Frontiers, Committee to Protect Journalists, Asiaweek and Businessweek.

The news portal has developed a reputation for providing a platform for academics and writers such as Jomo Kwame Sundram, Farish A. Noor, Faisal Tehrani, Uthaya Sankar SB and Wong Chin Huat to reach a wider audience.

[41] In November 2021, Malaysiakini reporter Wong Kai Hui won Thomson Foundation Young Journalist Award, chosen from almost 200 entrants from 55 countries.

In November 2023, academic Janet Steele published Malaysiakini and the Power of Independent Media in Malaysia, a book detailing the company's journey and impact.

[45] The top award in Malaysian journalism went to journalist S Vinothaa and the news lab team of Ooi Choon Nam and Affan Amrish Mohd Jalani for their contribution to the three-part series on how stateless children in Sabah have been forcibly taken from their parents and put up for adoption.

The award was granted to S Vinothaa, Ooi Choon Nam, Aidila Razak and Affan Amrish Mohd Jalani for their contribution to “Baby snatching: How stateless mums lose their infants in Sabah hospital”.

[48] While the co-founders have reduced roles in the daily running of the news portal, the duo continue to sit on Malaysiakini's board of directors and remain the company's largest individual shareholders.

[48] In October 2024, in advance of the company’s 25th anniversary, the new leadership of Anand and head of operations Tham Seen Hau announced a restructuring exercise which included job cuts.