The 61-year-old was only hired in January, but is expected to be relieved of his duties after the devastating loss in Lisbon.
Barca were completely overpowered by a ruthless Bayern side, who scored four times in either halves.
It is also Barcelona’s worst defeat since 1940, with substitute Philippe Coutinho rubbing salt in the wounds by scoring the last two goals against his parent club.
At full time Setien told reporters: “I’m not worried about my future right now, but a defeat that is very painful for the club and the fans.
“I know what a defeat of this calibre means.”