In 2020, an investigation by ProPublica into Turning Point USA's finances raised concerns about misleading financial claims, a lack of independent audits, and allegations that the organization's leaders enriched themselves while advocating for political causes.

Turning Point USA has faced widespread criticism for its 'Professor Watchlist' and 'School Board Watchlist,' which document educators' activities; critics argue these lists threaten academic freedom and have led to targeted harassment of teachers and professors.

Throughout the COVID-19 pandemic, Kirk faced intense criticism for spreading medical misinformation, including false claims about hydroxychloroquine and comparing vaccine mandates to apartheid, which led to a temporary suspension from Twitter.

Kirk and his organization faced scrutiny for their role in the events of January 6, 2021; Turning Point Action organized bus transportation for hundreds of supporters to Washington, D.C., for the rally that preceded the attack on the U.S. Capitol.

Kirk was frequently criticized by civil rights organizations, including the Southern Poverty Law Center, for rhetoric described as divisive, racist, and xenophobic, including his promotion of the 'Great Replacement' conspiracy theory and his public criticism of the Civil Rights Act of 1964 and Martin Luther King Jr.

Throughout his career, Kirk faced allegations that his organization violated federal rules for 501(c)(3) nonprofits by engaging in partisan political activity and providing financial support to conservative candidates running for student government and other offices.