During the celebrations of Argentina's Copa America triumph, the 23-year-old posted a video on Instagram that showed himself and several other national team players singing a song that involved racist language towards French people.
The song in question featured the words: "They play for France, but their parents are from Angola. Their mother is from Cameroon, while their father is from Nigeria. But their passport says French."
In the hours that followed, FFP president Philippe Diallo and Fernandez's Chelsea teammate Wesley Fofana hit out at the video, and it led to a public apology from the 23-year-old late on Tuesday night.
Furthermore, Chelsea have released an official statement to indicate that they had launched an 'internal disciplinary procedure' to determine how to handle the matter.
Split dressing room?
At a time when the majority of the Chelsea senior ranks are in pre-season training, the public response to the video has been limited.
However, it became apparent on Tuesday evening that Fofana, Malo Gusto and Axel Disasi - three of Chelsea's six-strong French contingent - had unfollowed Fernandez on Instagram.
On Wednesday morning, Fernandez is believed to have personally apologised to his teammates, seemingly triggering a show of support from Nicolas Jackson.
Nevertheless, Fofana has taken a different stance on the matter, releasing his own statement on social media to express his anger at the aforementioned video.
Unlike Jackson, Fofana has spent a season away from Chelsea and Fernandez, making it plausible that he is not as close or personable with the former Benfica man.
What now?
Through the reactions of their players, Chelsea have been made acutely aware that they must find an amicable solution for all concerned.
Selling Fernandez is not an option. In order to not make a loss with regards to amortisation, Chelsea would need to recoup £90m, which is unrealistic in the current market.
That leaves a scenario where club officials will hope that the French contingent at Stamford Bridge can continue to work alongside Fernandez both on and off the pitch.
Fernandez is not due to return to the squad for pre-season training for at least two weeks given his efforts for Argentina since the early part of June.