A series of reports in the German news magazine Der Spiegel has claimed City artificially inflated sponsorship deals in order to comply with UEFA's Financial Fair Play regulations.
City, who were fined £49 million ($63 million) after they were found to have breached the rules in 2014, have responded by saying they will not be commenting on the specific allegations.
The club claimed the criticism they have faced is an "organised and clear" attempt to damage their reputation.
Guardiola said on Tuesday he trusted the club's Abu Dhabi-based owners had acted honestly.
The City manager followed up by making it clear his players' record-breaking Premier League title triumph last season shouldn't be tainted by the claims, regardless of whether UEFA takes any further action.
"If they (the critics) want to undermine what we do, then no problem," Guardiola told reporters.
"We live our lives and what we achieve, it will remain in our hearts the rest of our lives.
"Like I said, I trust the people at the club and OK if there's something wrong we'll be punished.
"So whatever FIFA or UEFA say we were wrong, we will have to accept it. But I hear what my club said to me and I trust a lot of them."
City lead the Premier League going into Sunday's derby against arch rivals Manchester United.
They are nine points and six places above United in the table.
However, memories are still fresh of United's remarkable win at the Etihad Stadium in April, when they came from two goals down to win 3-2, forcing Guardiola to wait another week to win the Premier League title.
Paul Pogba scored twice in that game, after Guardiola had revealed in his pre-match comments that the France international had been offered to City in January by his agent.
Speaking before the latest Manchester derby, Guardiola said he had no regrets about those comments.
"I don't have too many regrets; that's the question for his agent, his comments. It's in the past," he said.
"Last season we lost, but every game is a new history and a new chapter.
"We realise how strong United are. When they dominate and create chances they win easily, but you can have the feeling you are in control and they can still punish you.
"It's Manchester United – with Liverpool, they are one of the strongest teams in England's history.
"I hope it can be a good derby and we can enjoy watching it."
Guardiola also laughed off a suggestion that his coaching is "better than sex".
The tongue-in-cheek comment was reportedly made by Paris Saint-Germain defender Dani Alves, who is currently promoting a documentary about his time at Barcelona playing for Guardiola.
Asked for his reaction, Guardiola said: "I prefer the sex... by far."
Alves is one of many players to have cited the City manager's coaching methods as inspirational, but Guardiola has played down the praise, making a passing reference to the struggles he had with former Sweden striker Zlatan Ibrahimovic at Barcelona.
"There is a list where they love me a lot, like Dani. I can see a huge list who are on the opposite side," Guardiola said.
"They have another side from Sweden and other places where they don't like me too much.
"Normally it happens when people don't play regularly – then they are not big fans. We try to convince them – sometimes yes, sometimes no," he added.