The midfielder - who cost in excess of £105m when signing from Benfica in January 2023 - has been representing Argentina at the Copa America.
Like he did at the 2022 World Cup, Fernandez played a key role in helping his nation win the trophy with victory over Colombia on Sunday night.
Although the 23-year-old will now take a break before participating in pre-season training, it appears that he will currently face a cold reception when he links back up with the squad.
In the aftermath of the success in the United States, Fernandez posted a video on social media of himself and his Argentina teammates chanting a racist song 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."
What has been the reaction?
FFF president Philippe Diallo quickly condemned the video, saying in a press release: "The President of the Federation Française de Football, Philippe Diallo, condemns in the strongest possible terms the unacceptable racist and discriminatory comments made against players of the French national team in the context of a song sung by players and supporters of the Argentina team after its victory in the Copa America and broadcast in a video on social networks.
"In view of the seriousness of these shocking remarks, which run counter to the values of sport and human rights, the President of the FFF has decided to take his Argentine counterpart and FIFA directly to court and to file a complaint for racially offensive and discriminatory remarks."
From Chelsea's perspective, though, the issue could have significant ramifications, with RMC Sport journalist Fabrice Hawkins saying on X that the French players at Stamford Bridge had been left 'very angry'.
That report has been confirmed by the public reaction of Chelsea defender Wesley Fofana, who took to social media to show and condemn the video with the caption of 'Football in 2024. Unabashed racism.'
There is also every indication that Fofana - as well as Malo Gusto and Axel Disasi - have unfollowed Fernandez on Instagram, the platform in which the video was posted.
Journalist Kieran Gill of the Daily Mail adds that Chelsea are taking the matter 'very seriously' and have launched an investigation.
What next?
Fernandez has seemingly put Chelsea in an extremely difficult position. At a time when harmony and cohesion is developing during Enzo Maresca's opening training sessions as head coach, the second most expensive player in the club's history has caused division.
In normal circumstances, Chelsea could perhaps look for a way out for Fernandez, but they would realistically need to take a massive hit financially to accommodate such a solution. Any interested clubs would also look to take advantage of it.
With Fernandez not due to start pre-season for at least two weeks, officials at the West Londoners have the task of trying to deal with the situation remotely.
Chelsea currently have six French players in the senior ranks, the other being Benoit Badiashile, Lesley Ugochukwu and Christopher Nkunku.