Future transfers in the Premier League will be subject to random spot-checks by investigators.
The move follows the final report by former Metropolitan Police commissioner Lord Stevens into alleged illegal payments.
His findings cleared all Premier League clubs of paying or receiving bungs but raised separate concerns about two managers and a number of agents.
The Premier League said they and the FA have agreed to carry out random spot-checks on future transfers using Quest investigators.
The league said in their report to clubs: 'With regards to the future, the Premier League and the FA have agreed to carry out a random audit of selected transfers from each window in order to further ensure compliance.
'The Premier League will be asking Quest to assist them in this and it may transpire that this becomes a joint initiative subject to agreement with the FA.'
Stevens expressed concerns over 'a conflict of interest' involving Sam Allardyce and his former agent son Craig while at Bolton.
He also points to 'inconsistencies in evidence' provided by former Newcastle manager Graeme Souness.
Deals involving Chelsea, Newcastle, Bolton, Middlesbrough and Portsmouth have all been highlighted by Quest in their final report to the Premier League.
The main focus of the report targets agents although the clubs are set to face a further investigation from the Football Association.
Stevens expressed concern about 15 agents and third parties involved in some 17 transfers.
He said in the report: 'The inquiry remains concerned at the conflict of interest that it believes existed between Craig Allardyce, his father Sam Allardyce the then manager at Bolton Wanderers and the club itself.'
He went on: 'There remain inconsistencies in evidence provided by Graeme Souness a former manager of the club and Newcastle chairman Freddy Shepherd's son Kenneth Shepherd as to their respective roles in transfer negotiations.'
Souness was baffled to be named. He said in a statement issued by his solicitors: 'I cannot understand why my name features in this report.
'I volunteered full information to Quest as a witness and I have heard nothing further from them.'
Of the 17 transfers named by Stevens, all remain under investigation because of unsatisfactory responses from agents - including super-agent Pini Zahavi.
Four relate to Newcastle signings (Emre Belozoglu, Jean Alain Boumsong, Amady Faye, Albert Luque), four to Bolton (Ali Al-Habsi, Tal Ben Haim, Blessing Kaku, Julio Correia), three to Chelsea (Didier Drogba, Petr Cech, Michael Essien), three to Portsmouth (Collins Mbesuma, Benjani Mwaruwari, Aliou Cisse), two to Middlesbrough (Ayegbeni Yakubu and Fabio Rochemback), and one remains undisclosed.
Zahavi's lawyer Ehud Shochatovitch said: 'My client believes he has been targeted because he is successful and enjoys a high profile in the football world.'
The Premier League will now send the findings to the FA and FIFA who will decide whether to take disciplinary action.
An FA spokesman said: 'The FA will give full consideration to its contents and the documentation that is due to be passed on by the Premier League and Quest.
'We will now go through their information as part of our governance and regulation process. This will determine what action is required.'