The Gunners were taking part in their first International Champions Cup game of their tour of the USA on Wednesday night in Los Angeles.
After Emery fielded a youthful side in the 3-0 win over Colorado Rapids earlier in the week, the Spaniard decided to play several senior stars for the clash with the German champions.
Pierre-Emerick Aubameyang, Alexandre Lacazette, and Mesut Ozil all started, as did Granit Xhaka and Ainsley Maitland-Niles.
But it was the inclusion of Mustafi into the starting line-up that irked many Arsenal fans.
The German has been branded a laughing stock by many Gunners fans in recent times after a host of terrible performances in defence.
Rumours about him leaving the club have resurfaced once again in the summer transfer window but he insists he wants to remain.
Mustafi was handed the captain’s armband in the win over Colorado, much to the amusement of fans after he was pictured placing it around his arm upside down.
One notable exclusion from the team against Bayern was that of Nelson, who also did not start against Colorado.
“I’ve stayed up to watch Mustafi play but not Nelson”
While he came on for Henrikh Mkhitaryan in the second-half, fans were not happy at him being left out with Mustafa starting again.
One fan wrote: “I’ve stayed up to watch Mustafi play but not nelson ������.”
While another said: “If I’ve said it once I’ve said it one hundred times :no nelson no party.”
“Mustafi in the lineup and Nelson on the bench, whaaaaaaat,” wrote another irked fan.
Another wrote “Mustafi ffffsss,” while another said simply said “I’m going to bed.”
Mustafi ended up playing the full game with Arsenal winning the game 2-1.
A 49th minute Louis Poznanski own-goal had given Emery’s men the lead before Robert Lewandowski equalised with 20 minutes left.
Then Edward Nketiah netted the winner for the Gunners with two minutes remaining.