The Bavarians have been without a number of first-team stars in recent weeks with Holger Badstuber, Javi Martinez and Thiago Alcantara all absent while Mario Gotze and Bastian Schweinsteiger have been struggling for fitness.
But Guardiola has fired a warning to other Bundesliga sides, insisting that his team can only improve on their early-season showings - if they correctly carry out his instructions.
"I am convinced that we will be even better when all the players are fit," he told the club's official magazine.
"But we will only be in the hunt for titles at the end of the season if each player accepts my decisions in this great squad.
"Otherwise, we have problems. I am a great friend of my players when they accept what I say. I support those who accept my decisions but those who do not want to understand will sit in the stands. I say again: we need all of our players.
