Jose Mourinho is still missing key players like Paul Pogba and Romelu Lukaku but the performance in the Allianz Arena was not one to inspire confidence that it will be all right on the night when Leicester visit Old Trafford on Friday.
Made a number of saves in the first half, most notably to deny Thiago and Serge Gnabry, but they were saves he was expected to make.
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By Mourinho's logic Bayern, with three preseason games under their belt compared to United's five, should be playing catch-up in terms of preparation for the new season.
The France international's future has been a source of relentless speculation over the past few months following a hard second season under Jose Mourinho. At the other end Manuel Neuer could have happily watched from a deckchair.
There are major question marks over Martial's future at Old Trafford after speculation that the French global wants to leave the club and boss Jose Mourinho's criticism that the 22-year-old did not return to training quickly enough following the birth of his second child.
The returning Marcus Rashford played 65 minutes and Fred impressed in midfield but Jose Mourinho will be sweating over the fitness of Eric Bailly, who hobbled off in the second half.
Niko Kovac showed little interest in settling at half-time with Jerome Boateng, Robert Lewandowski and Leon Goretzka introduced off the bench, yet the goal came from an unlikely source as midfielder Martinez calmly guided a glancing header beyond a helpless De Gea.
Javi Martinez headed home a second-half victor to give Bayern victory in a match they dominated. "Or they already have fantastic squads like Chelsea, Spurs or Manchester City".