[13][14] The change in ownership structure came at a time when the South African Clothing and Textile Workers Union (SACTWU) had sued Sekunjalo Independent Media in the Western Cape High Court for failing to repay a loan of ZAR 150 million plus interest in aid of funding the purchase of the company from Tony O'Reilly.

In 2023, Independent Media issued retrenchment notices to its staff for the fifth time since Sekunjalo's purchase of the news organisation.

[19][20] By October 2023, at least a third of staff were retrenched and the company failed to pay severance packages on time and instead issued grocery vouchers to the value of ZAR 2500 which initially were not loaded with any cash.

[21][22] At the end of 2023, Group CEO of Independent Media unexpectedly resigned after 16 months in the job prompting Survé to again take up an executive role in the company.

[25][26] According to The Economist, IOL "often engages in 'information laundering' designed to make sentiment appear homegrown, says Herman Wasserman at the University of Cape Town.

[5][30][31] In 2021, IOL published a series of articles about a Tembisa woman having delivered decuplets (ten babies) which were penned by Pretoria News editor Piet Rampedi.

The story was debunked as fake news as no evidence of the births was available and multiple requests for donations were made both in print and online Independent Media platforms.

[36] On 15 July 2024, Independent Media and IOL held a press conference in Cape Town, titled "The Unmasking Project", where they claimed to reveal the identity of an anonymous X user known only as Goolam (@goolammv).

Former cabinet minister, Lindiwe Sisulu, also shared her views on the anonymous X account, claiming that it was responsible for her failure to be elected ANC president at the party's conference in 2017.