The Spaniard has enjoyed a fantastic start to his career at the Allianz Arena, guiding the side to the top of the Bundesliga standings, despite his squad having suffered injuries to the likes of Bastian Schweinsteiger, Mario Gotze and Thiago Alcantara during the campaign.
But Guardiola is keen to stress that he believes his side can improve their performances on the pitch, and warned anyone who does not accept his philosophy will find themselves on the substitutes bench.
"I am convinced that we will get better when all the players are fit," he told Bayern Magazine.
"But we will only fight for titles at the end of the season if every player in this excellent squad accepts my decisions. Otherwise we'll have problems.
"I am a great friend of my players when they accept what I say. Whoever accepts my decisions I support, but whoever does not want to understand will often sit on the bench.
"I say again and again we need every one of our players. And therefore I'll be happy when all of them are available."
Guardiola's only competitive defeat came in July's 4-2 loss to Borussia Dortmund in the DFL-Supercup.
And he admitted he did not expect his team to adapt to his style so soon.
He added: "Honestly it has surprised me a bit, how quickly the players have taken on my ideas. I thought we would clearly need more time for that, but the level is already very, very high.
"Of course not in every game and also not through a complete 90 minutes, but as an initial conclusion from the first quarter of the season I can say I am happy with what we are showing on the pitch."
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