The chaos at Arsenal laid bare by Granit Xhaka’s angry reaction to being booed by supporters is just the tip of the iceberg for a club on the brink of crashing into crisis and facing the threat of losing star players at the end of the season.

Head coach Unai Emery met with Xhaka on Monday and will consult with members of his Arsenal squad over whether or not the midfielder can continue as captain after responding to jeers following his substitution in the 2-2 draw with Crystal Palace.

But Telegraph Sport understands Emery is facing even bigger challenges as he attempts to keep Arsenal in contention for a top-four place that he needs to save him from the sack.

Other than costing Emery his job, failure to qualify for the Champions League will leave Arsenal with a huge fight to convince strikers Alexandre Lacazette and Pierre-Emerick Aubameyang to stay at the Emirates.

Arsenal have been attempting to negotiate new contracts with Lacazette and top scorer Aubameyang. But one victory in their last four Premier League games has seen Arsenal fall four points behind fourth-placed Chelsea and raised question marks over their bid to satisfy the pair by securing a place in next season’s Champions League.

Emery is not only facing a fight to ultimately save his job, but also to convince his squad that he is the right man to take them forwards.

The Spaniard’s decision making and muddled instructions have left a number of players confused and splits have begun to appear over the handling of Mesut Özil, who has been frozen out, and summer signing Nicolas Pépé.

Özil has made just one Premier League appearance this season and has not been part of Emery’s last six squads, while Pépé has started the last eight Premier League games despite only scoring once from the penalty spot since signing from Lille for £72 million.

Emery last week revealed that he received the board’s backing to freeze out Özil and a source told Telegraph Sport: “You’ve got to wonder who is making the decisions. Has the coach been told not to play Özil or does he have a problem with the player?

“Probably a bit of both, but it is damaging the team because Arsenal are not creating a lot of chances and Özil is clearly good enough to play in some games.

“You also have to wonder why Pépé is starting every game. He was an expensive signing for the club, so does Emery have to start him or does he want to?

“It may be that he is feeling pressure to do what the board wants, but he has to be strong and make his own decisions. It is creating a strange atmosphere within the squad because nobody is really sure what is going on.”

Nicolas Pépé receives instructions from Emery during a training session at London Colney credit: Getty Images

It had appeared that there might be a statement from Arsenal on Xhaka, but it is understood that Emery will instead address the issue on Tuesday ahead of the Carabao Cup fourth-round tie away to Liverpool.

Xhaka's outburst came with director Josh Kroenke in attendance at the Emirates while his father, Stan, was also in London but was at Wembley to watch his Los Angeles Rams American football team beat the Cincinnati Bengals.

Josh Kroenke is understood to have gone to see Emery in his office after the Palace game, but there was nothing unusual in that as it is what he would normally expect to do when he goes to an Arsenal home game.

Emery is expected to continue in his job while Arsenal are in contention for a top-four place, but is likely to go at the end of the season if his team falls short.

Héctor Bellerín, Arsenal's third captain behind Xhaka and Aubameyang, did not play in the game as he continues to manage his return following a serious knee injury but he posted his support on Twitter on Monday morning.

“We are all humans, we all have emotions, and sometimes it's not easy dealing with them. It's time to lift each other up, not to push each other away. We only win when we are together,” Bellerín said.

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The Arsenal official photographer Stuart McFarlane also posted on social media with a series of photographs showing Lucas Torreira supposedly in tears at the abuse directed at Xhaka.

“Didn’t want to post these pictures but I felt I had to,” McFarlane wrote. “This is Lucas Torreira’s emotional reaction to the abuse Granit Xhaka received after his substitution, in tears and inconsolable. Absolute love and respect for his captain.”

Xhaka is a popular member of the squad and stripping him of the captaincy would risk further issues for Emery. But his decision to use a player vote to decide the Arsenal captaincy was not universally popular.

A source said: “Again, what is happening and who is in charge? Xhaka may be popular, but the head coach should be making these decisions not the players.

“And now do the players choose whether or not Xhaka keeps the captaincy? Emery needs to give the squad some clarity and show he can manage because, if he doesn’t, there are much bigger problems around the corner.”