HMRC investigators claimed back £124.8m in unpaid tax from Premier League clubs in the year to 31 March 2023.
Reclaimed payments included National Insurance on agents' fees and image rights, plus tax on benefits in kind.
"We will continue to carefully scrutinise arrangements between clubs, players and agents to ensure the correct tax is paid," said HMRC.
"We work closely with the football industry to educate and deal with tax risk head on."
Benefits in kind included flights and hotels for Premier League players and families.
Elliott Buss, of UHY Hacker Young, said HMRC was "really cracking down on the football industry".
He added: "HMRC now have these clubs' tax affairs in their sights.
"The growing proportion of agents' fees being paid by clubs is drawing the attention of the taxman to the possibility that not all tax due on these payments is being paid."