The APT rules were introduced in December 2021 after the Saudi Arabian-led takeover of Newcastle earlier that year and were amended in March and November 2024.
The rules were successfully challenged by Manchester City last year.
A tribunal then ruled low-interest shareholder loans should not be excluded from the scope of the APTs, and that changes made to toughen up the regulations also breached competition law.
Following the ruling, City criticised the Premier League’s “misleading” suggestion the regulations could be swiftly amended – and threatened further legal action if there was a “knee-jerk reaction”.
City insisted the league’s proposed changes “would introduce into the rules a retrospective exemption for shareholder loans… one of the very things that was found to be illegal in the recent arbitration”.
They said there should be no vote on changes before a further determination by the panel.
However, the Premier League voted through the amendments despite opposition from Newcastle United, Nottingham Forest and Aston Villa, as well as City.
The Premier League and City attended a two-day hearing earlier this year to make submissions in relation to the impact of the original ruling.
They have now reached a settlement that will bring to a close a long-running legal battle that cost both sides millions of pounds in legal fees.