The boss revealed the popular Portuguese playmaker was physically and mentally exhausted at times in the previous campaign.
But Pep says he believes we will see a different Bernardo during 2020/21.
“Last season he was injured for some minutes and he did not reach the level of previous seasons, but it happens.
“The year we won four titles, it was incredible the way he played and then he won the Nations League with Portugal and was player of the tournament.
“If there is one player I have no doubts about it is Bernardo.
“But he didn’t have time to refresh, he was exhausted and his mind was exhausted. He struggled with this.
“The NBA is the world’s best league in basketball and the Premier League is one of the best in football.
“The NBA can have many games in a season, but hey have a three or four months break, where we have two weeks
“It's too much. Hopefully with new ideas of Premier League they can protect the quality.
“So, last season, Bernardo was tired mentally, but this time, I have the feeling he's going to have a very good season.
“He is already showing us many things we saw in the past.”
Looking ahead to Saturday’s clash with Arsenal, the boss admitted he is expecting a difficult afternoon.
City are looking for a second Premier League win in four games, having lost to Leicester and drawn with Leeds since the opening day win over Wolves.
The Gunners represent yet another tricky game for Pep’s men – and says the FA Cup semi-final proves what a positive impact Mikel Arteta has had at the Emirates.
“They showed how good they are,” he said. “They showed us they had more desire to reach the final.
“For them it was so important to reach the final, but for us it was just a semi-final and they played with more desire.
“I told them (the players). They know it and they agreed; the second half was better, but it was not enough.
“We have to play the first minute to 95th minute.
“Arsenal are always a good team, now especially tomorrow, we have a chance to find ourselves and find who we are as a team.
“We were able to make a good 65 mins against Wolves, a good 25 mins against Leicester and good first 35 and last 15 mins at Leeds, but we were not able to sustain 90 minutes at a high level.”