Martinez, who cost the Bavarian club €40 million [£34.5m] in the summer, did not feature against Wolfsburg on Friday due to a bruised toe.
But after completing a training session on Saturday, Bayern coach Jupp Heynckes was happy with his progress and now believes Martinez could take part in the first leg of the last 16 clash.
“The way it looks at the moment, he’s in contention for selection,” Heynckes told FCB.tv.
The news that Martinez should be fit for selection follows Bayern losing Holger Badstuber to injury and Jerome Boateng to suspension ahead of the trip to the Emirates.
Martinez has been a mainstay of Bayern’s midfield this season, playing 19 games and scoring one goal.