The FA was told explicitly of a second separate investigation into Mark Sampson just months into his job as England head coach, ITV News understands.
Rumours about Sampson's behaviour were investigated in 2012 during his previous job as the Bristol Academy women’s football manager at South Gloucestershire and Stroud College (SGS).
According to ITV News sources, SGS shared the details of their own inquiry when the FA itself began looking into a complaint about Sampson's time in Bristol, shortly after they made him England boss.
A source at the College told us: “We fully cooperated with the FA investigation, and we disclosed the previous rumour to the investigation team.
"We were not told if the two issues were connected.
"We have heard nothing more from the FA about the investigation.”
The FA probe only came to light earlier this week in the wake of Sampson being sacked for what the organisation described as “inappropriate and unacceptable behaviour by a coach” during his time in Bristol.
The behaviour was detailed in the FA’s own inquiry in 2015 which cleared Sampson of being a safeguarding risk.
What the FA hasn't revealed is that the authors of that report were also alerted to a separate 2012 investigation into the Bristol rumours.
If so, that means the FA knew theirs was not the first and only investigation into their high-profile manager.
Asked to respond on Friday, a spokesman for The FA said: "This is part of a confidential process so we can't make any comment."
ITV News understands that in 2012 in Bristol the safeguarding team was informed about rumours concerning Sampson's relationships with Academy players and carried out a preliminary investigation.
We have learnt that no one questioned during that process was prepared to sign a formal witness statement.
There has never been any suggestion or allegation that what was rumoured to have taken place could have been considered a criminal offence.
Following discussions with the Local Authority Designated Officer it was judged there was no case to answer and the matter was closed as a result.
Mr Sampson has so far not responded to several attempts by ITV News this week to contact him.