Emery allowed his players to vote on who should wear the armband following the summer departures of Laurent Koscielny and Petr Cech.
But Emery insists that the Switzerland international was the right man for the role.
“The main captains last year were Koscielny, Cech, [Aaron] Ramsey and Nacho Monreal and they all left the team,” the Spaniard told BBC Sport.
“So the natural leader in the changing room, because of his values and what he represented, was Granit Xhaka. There was a vote to see if what I felt about him was also felt by the players, and they did.
“Circumstances meant that Xhaka had a clash with fans, but he is the leader that this team needs then and now, because of the values he represents, because of the respect everyone had for him and because of his experience.
“But from the moment he stops being captain, there are other players who also have the capacity to take over, like [Pierre-Emerick] Aubameyang, [Mesut] Ozil, [Alexandre] Lacazette but the hierarchies within a team have to be established with values, the strength of the squad and also what happens on the pitch.
“The coach has to let things flow naturally and allow the leadership to be established. Logically, I am the one who decides who will be the captain, but the players get to tell me who they perceive as captain.
“What made it difficult was that the four principal captains left and new people had to take on the responsibility.
“These things need a process of settling and adjusting to wearing the armband that is very important to me and very necessary for this transition to take place.”