The Gunners face the Championship side at the Emirates Stadium just four days before the Champions League last-16 tie against the Bundesliga giants.
Mertesacker admits that Arsenal are desperate to advance in the FA Cup and will delay preparation for the Bayern game until Sunday.
"We still have an important cup game on Saturday - we absolutely want to advance in the FA Cup, that is why the preparations for Bayern are not that intense yet," the 28-year-old revealed on the adidas football Hangout on air webchat.
"However, beginning on Sunday the preparations for Tuesday's match will be extreme.
"Bayern are doing superb this year and that is a big challenge for us, but we are looking forward to both legs."
Mertesacker joined Arsenal from Werder Bremen in 2011.