Emery admitted that he informed Xhaka of his decision to remove him from his "leadership group" and replace him with Pierre-Emerick Aubameyang as captain on Tuesday morning, and now it looks like his Arsenal career is over.
"I have spoken to Granit and he is no longer one of the captains in the group", Emery said at a news conference to preview Wednesday's game.
Arsenal failed to move within a point of qualification to the Europa League knockout phase after a 1-1 draw at Vitoria Guimaraes.
The 27-year-old Switzerland worldwide has been left out of the squad for the match.
'The decision I took I told him and I told the other captains, and now it's continuing, ' he said.
Arsenal travel to Portugal with a fully fit squad but still, a number of youngsters are expected to be named in the first XI with perhaps only the defensive line seeing seniority.
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If Arsenal get rid of on Saturday then Merson feels Emery should really be fearing for his work and he has informed the club they will have to do every thing in their energy to entice Rodgers to come to be his successor.
"This competition for us is very important and if we win tomorrow we are going to be the first in the table".
The unusual kick-off time of 3:50 p.m. local time on a Wednesday led to the game being played in a half-empty stadium.
The Gunners have used a combination of senior and young players in each match, but have left out top scorer Aubameyang and World Cup victor Ozil, who has only been selected four times in 2019-20.
That result would also spell the end of Vitoria's European campaign, as they have only one point from four matches. If I were Arsenal, I'd be breaking the bank to get him, give him a five-year contract and sit back and watch him transform the club, " he added.