The Portugal international has played an integral role in City's success under Guardiola but has been linked with a move to Barcelona this summer and the coach admitted that the decision is out of his hands.
Guardiola said: "In the end, sometimes the club, sometimes the player, sometimes the agent, many reasons, sometimes you have to divide our path.
"I've said many times the desire of the player is the most important thing; I want people happy here trying to do it together. Of course, I would love for Bernardo to continue here, he is a special player in the dressing room for me, but I don't know what is going to happen. Honestly, I don't know.
"What is going to happen will happen and if he stays it's perfect, and if he has to leave it's because football is like this, the clubs have an agreement, the player has desires, and I am not the person to stop the desire of people."
Guardiola is hopeful that Bernardo will choose to stay but can understand why footballers want to test themselves in different environments.
He said: "I want the best for the players, but I want Bernardo to stay, definitely, 100 per cent, I want him to stay here.
"But, at the same time, if you want to leave and have an offer and the clubs have an agreement, it's common sense what I said, it's nothing special, this is the reality.
"He's an important player for me, Bernardo is special. I don't know what is going to happen. As far as Manchester City know, we didn't get any offer, last season either, this is what I can say. Bernardo is ready, he's training really well, he's ready for Sunday and that's all."