A Comptroller Auditor-General report revealed that Pachaiyappa's College in Chennai collected ₹2,14,678 in excess application fees compared to government-prescribed limits, raising concerns over fee transparency and potential exploitation of economically vulnerable students.

Students at Pachaiyappa's College staged a protest on January 24, 2025, urging the Tamil Nadu government to take over the administration of the college due to mismanagement, inadequate facilities, and undue interference by the trust managing the institution. The protest reflects growing concerns over authoritarian control within the college administration and calls for increased public accountability.

Nearly 100 students protested against the college management for using unfair administrative practices, including the suspension of a student protester and retaining a secretary beyond his tenure. The protest calls for greater transparency, democratic decision-making, and accountability from the college trust and management.

On January 23, 2025, students at Pachaiyappa's College staged a protest demanding that the state government take charge of the college's administration from the trust. They cited mismanagement, lack of basic amenities, and unnecessary restrictions on their activities, calling out an overreach from the trust's board.

The Madras High Court quashed a charge sheet filed against 38 teaching and non-teaching staff of Pachaiyappa's College. The charge sheet had been filed following a protest during a college committee meeting overseen by a court-appointed interim administrator in April 2019. The ruling protects staff rights to protest and underscores the judiciary’s role in safeguarding labor rights and dissent.

A new policy implemented at one of the self-financing colleges under Pachaiyappa’s Charitable Trust has barred qualified teachers—despite holding advanced degrees—from applying for assistant professor positions if their postgraduate education was completed via distance learning. The policy, effective on May 11, 2023, has led to several experienced educators being excluded from the recruitment process.

A judicial order initially terminated the appointments of 254 assistant professors recruited by Pachaiyappa’s Trust, citing widespread recruitment irregularities, but a division bench later stayed the termination pending appeal. The decision has raised concerns about due process and the rights of academic staff.

Pachaiyappa's Trust Board issued show-cause notices to 152 faculty members appointed across six colleges after it was revealed that many appointees were unqualified. The irregular selection process has raised concerns about undermining merit, compromising educational standards, and disadvantaging candidates from economically weaker sections.