The record German champions are back in action against Mainz on Saturday, starting an intense period of games leading up to the winter break which includes Bundesliga, DFB-Pokal and Champions League commitments.
Squad rotation for such a marathon is inevitable and Guardiola hopes his players will respect his decisions without questioning them.
"I'm a big friend of my players, as long as they accept what I have to say," Guardiola said in the club's matchday magazine.
"Anybody who accepts my decisions receives my support, but whoever does not want to understand them will often find themselves sat in the stands."
Guardiola is going to be faced with several difficult decisions as his treatment room empties.
With Mario Gotze back in the frame to face Mainz and both Javi Martinez and Thiago Alcantara closing in on returns, he soon may have his full squad available.
That means top players such as Arjen Robben, Thomas Muller and even Bastian Schweinsteiger may have to do time on the bench.
"When all of our players are fit, then we can get even better," Guardiola said.
"But we can only be fighting for titles come the end of the season if all of the players in this fantastic squad accept my decisions.
"Otherwise, we'll have problems."
Those are problems Mainz coach Thomas Tuchel would be more than happy to face.
His side have picked up just one point from their past five games, and that is with all their key figures available.
"This is a very uneven duel," he said at a press conference.
"If we really want to get anything out of it, then certainly a lot of things have all got to come together. We've got to be at our very, very best."
However, in spite of the declared inferiority of his side, Tuchel has warned Bayern not to expect anything for free.
"We're not gifting them anything," he said. "Of course we also have to hope that Thomas Muller heads wide of an open goal, but I can't imagine him doing that again after Leverkusen.
"But I have no fear.
"I know what competition we are playing in and this is like a Champions League game for us, and I'm definitely looking forward to it."