Chelsea have been fined £10 million and given a suspended ban from registering new players for two transfer windows for breaching rules relating to payments to agents between 2009 and 2022.
But the club have had a six-point deduction, which was suspended until 30 June 2027, "set aside" on appeal.
Owners Todd Boehly and Clearlake Capital self-reported 74 breaches of Football Association rules when they purchased the club in 2022.
Chelsea admitted making £47 million in secret payments to unregistered agents and third-parties over transfers between 2011 and 2018.
The FA said it was "continuing to investigate individual misconduct arising out of this case".
The fine was set to be £26m, but was reduced by a third to £17.25 million for self-reporting and what the regulatory commission's written reasons described as the "exceptional and unprecedented nature" of co-operation, which "amounts to mitigation".
It was then cut by another third to £11.4 million for an early guilty plea, then to £10m because of fines already given to the club by Uefa and the Premier League.
The FA said it was "an appropriate penalty" that would punish the club and also "deter similar misconduct and maintain the integrity of the game".
Manchester City's hearing over the 115 charges they face took place towards the end of 2024, but a verdict is yet to be announced.
The number of charges and severity of the accusations are among the reasons the case has taken as long as it has.
The £10m Chelsea have been fined will be invested into grassroots football.
The regulatory commission said: "Had the club not brought these matters to the attention of the FA, it is unlikely that they would have been discovered."
It added the initial points deduction had been suspended because the FA did not ask for one and the Premier League did not impose one.
"Now the FA process has concluded, this brings all regulatory proceedings against the club to a close," a Chelsea statement read.
"We are grateful to Uefa, the Premier League and the FA for their engagement with the club throughout these processes."
In March, Chelsea were given an immediate nine-month academy transfer ban and a £750,000 fine over the registration of academy players between 2019 and 2022.
All of the breaches relate to the period when Roman Abramovich was owner of Chelsea.
Abramovich was sanctioned by the UK government in March 2022 over alleged links to Russian president Vladimir Putin - something he has denied.
He was granted a special licence to sell Chelsea following Russia's invasion of Ukraine, providing he could prove he would not benefit from the sale.
The 59-year-old said funds from the sale would be donated via a foundation "for the benefit of all victims of the war in Ukraine", which would include those in Russia.
The £2.5bn in proceeds have been frozen in a UK bank account since the sale. Abramovich does not have access to the money but it still legally belongs to him.
In 2023, the BBC reported leaked documents revealed a money trail linking Abramovich to two men dubbed "wallets" of Putin.
BBC Newsnight, BBC Verify and Panorama partnered with the Bureau of Investigative Journalism to uncover the revelations as part of Cyprus Confidential - a global investigation led by reporters at the International Consortium of Investigative Journalists (ICIJ) and Paper Trail Media.
The reports alleged the leaked documents from Cyprus revealed new evidence linking the former Chelsea owner to a secret £26m deal in 2010.
Abramovich has previously denied any financial relationship with the Russian leader.
In June, the Government threatened to sue Abramovich to make sure the money from the Chelsea sale went to Ukrainian humanitarian aid - rather than "all victims of the war in Ukraine" as Abramovich had said.
Two months before selling Chelsea in May 2022, Abramovich was said to have suffered from suspected poisoning at peace talks on the Ukraine-Belarus border.
The Russian billionaire, who made his fortune in oil and gas, was reported to have a role as a broker in talks between Ukraine and Russia.
But the club have had a six-point deduction, which was suspended until 30 June 2027, "set aside" on appeal.
Owners Todd Boehly and Clearlake Capital self-reported 74 breaches of Football Association rules when they purchased the club in 2022.
Chelsea admitted making £47 million in secret payments to unregistered agents and third-parties over transfers between 2011 and 2018.
The FA said it was "continuing to investigate individual misconduct arising out of this case".
The fine was set to be £26m, but was reduced by a third to £17.25 million for self-reporting and what the regulatory commission's written reasons described as the "exceptional and unprecedented nature" of co-operation, which "amounts to mitigation".
It was then cut by another third to £11.4 million for an early guilty plea, then to £10m because of fines already given to the club by Uefa and the Premier League.
The FA said it was "an appropriate penalty" that would punish the club and also "deter similar misconduct and maintain the integrity of the game".
Manchester City's hearing over the 115 charges they face took place towards the end of 2024, but a verdict is yet to be announced.
The number of charges and severity of the accusations are among the reasons the case has taken as long as it has.
The £10m Chelsea have been fined will be invested into grassroots football.
The regulatory commission said: "Had the club not brought these matters to the attention of the FA, it is unlikely that they would have been discovered."
It added the initial points deduction had been suspended because the FA did not ask for one and the Premier League did not impose one.
"Now the FA process has concluded, this brings all regulatory proceedings against the club to a close," a Chelsea statement read.
"We are grateful to Uefa, the Premier League and the FA for their engagement with the club throughout these processes."
In March, Chelsea were given an immediate nine-month academy transfer ban and a £750,000 fine over the registration of academy players between 2019 and 2022.
All of the breaches relate to the period when Roman Abramovich was owner of Chelsea.
Abramovich was sanctioned by the UK government in March 2022 over alleged links to Russian president Vladimir Putin - something he has denied.
He was granted a special licence to sell Chelsea following Russia's invasion of Ukraine, providing he could prove he would not benefit from the sale.
The 59-year-old said funds from the sale would be donated via a foundation "for the benefit of all victims of the war in Ukraine", which would include those in Russia.
The £2.5bn in proceeds have been frozen in a UK bank account since the sale. Abramovich does not have access to the money but it still legally belongs to him.
In 2023, the BBC reported leaked documents revealed a money trail linking Abramovich to two men dubbed "wallets" of Putin.
BBC Newsnight, BBC Verify and Panorama partnered with the Bureau of Investigative Journalism to uncover the revelations as part of Cyprus Confidential - a global investigation led by reporters at the International Consortium of Investigative Journalists (ICIJ) and Paper Trail Media.
The reports alleged the leaked documents from Cyprus revealed new evidence linking the former Chelsea owner to a secret £26m deal in 2010.
Abramovich has previously denied any financial relationship with the Russian leader.
In June, the Government threatened to sue Abramovich to make sure the money from the Chelsea sale went to Ukrainian humanitarian aid - rather than "all victims of the war in Ukraine" as Abramovich had said.
Two months before selling Chelsea in May 2022, Abramovich was said to have suffered from suspected poisoning at peace talks on the Ukraine-Belarus border.
The Russian billionaire, who made his fortune in oil and gas, was reported to have a role as a broker in talks between Ukraine and Russia.
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