The French midfielder acknowledges the threat posed by the Champions League holder, but says the Gunners will "try to play our best football to try to win the game."
Pep Guardiola replaced Heynckes in the summer and while Flamini knows the Bavarians will pose a stern test, he says Arsenal will go all out to progress to the next round.
"We know it won't be an easy game because Bayern are a strong, strong team, but we are Arsenal, we have big ambitions," he told reporters.
He went on to say that his side would be trying to produce its best game against the German club.
"We will do everything, we will try to play our best football to try to win this game or to get a good result," he said. "It is tough to win a title. You have to fight for every game and we are trying to do it."
Flamini, speaking after the Gunners knocked Liverpool out of the FA Cup on Sunday, insists the club is pushing to win three competitions.
"What I can say is, this year, Arsenal have a big ambition and are fighting for the [Premier League] title," he added. "We have qualified in the FA Cup and we will do everything to qualify in the Champions League. We know it will be a difficult game and now it is important to recover very well because we had so many games.
"We had difficult games and when we had to fight and compete in these games, we did. We have had a lot of victories away and that is very positive for us. I think the commitment this year is very important, it is very good. We have shown character and solidarity.
"We have a collective of players and we need everyone because we want to win a title."