UEFA has opened disciplinary proceedings against Real Madrid, Barcelona and Juventus as they seek to punish the European Super League rebels.
The trio could be expelled from the Champions League for two years as a consequence.
The two LaLiga and one Serie A club are the only three of the original 12 who signed up for the breakaway competition not to have formally withdrawn.
A UEFA statement read: 'In accordance with Article 31(4) of the UEFA Disciplinary Regulations, UEFA Ethics and Disciplinary Inspectors have today been appointed to conduct a disciplinary investigation regarding a potential violation of UEFA's legal framework by Real Madrid CF, FC Barcelona and Juventus FC in connection with the so-called 'Super League' project.
'Further information regarding this matter will be made available in due course.'
The two-year ban from Europe's leading club competition is the harshest sanction at UEFA's disposal.
The prospect of disciplinary action appeared inevitable last Friday when a statement confirming the peace accord with nine of the clubs ended: 'UEFA has reserved all rights to take whatever action it deems appropriate against those clubs that have so far refused to renounce the so-called 'Super League'.
'The matter will promptly be referred to the competent UEFA disciplinary bodies.'
The three clubs were driving forces behind the hatching of the Super League plan, which emerged on April 18.
Backed by around Â£3billion in funding by American bank JP Morgan, the idea was to create a new midweek competition with at least 12 founder members who could not be relegated from it.
Six Premier League clubs - Manchester United, Manchester City, Arsenal, Chelsea, Liverpool and Tottenham Hotspur - as well as Barcelona, Real Madrid and Atletico Madrid from Spain and the Italian trio of Juventus, Inter Milan and AC Milan signed up as founder members.
However, the six English teams withdrew from the plans 48 hours later following a furious backlash from fans. Inter, AC Milan and Atletico later backed away from the plans.
The other nine clubs agreed a peace deal with UEFA on Friday and will forfeit five per cent of prize money from European competitions for one season, starting in 2023-24.
They will also make a combined Â£13.4million goodwill donation to the UEFA Foundation.
They also accepted they will be fined 100 million euros (Â£86.9m) each if they attempt to join an unauthorised competition in the future.
The nine were accepted back into the UEFA fold and also the European Club Association.
Things could get even worse for Juventus after they were also threatened with expulsion from Serie A if they donâ€™t withdraw from the Super League.
Italian Soccer Federation president Gabriele Gravina said on Monday: 'The rules are clear. If Juventus is still part of the Super League when it enters next season, it can't participate in Serie A.'