On Friday news broke that City had been found guilty of the majority of 115 charges they faced, immediately sparking speculation they could face unprecedented sanctions.
Pochettino, who was in charge at Spurs between 2014 and 2019 and Stamford Bridge in 2023-24, having previously been at Southampton from 2013 to 2014, said it warped the view of history.
Pochettino told the Guardian, through an interpreter: "At the end of the day, we went through something where sporting fairness didn't exist, so how do you repair everything that was damaged because of that?
"If it's true ... we've lived through a period of deception."
Pochettino said there was no punishment which could make up for the "damage" which had been caused.
"Whatever punishment, it's impossible to turn back time," he added.
"It's done a lot of damage. At the end of the day many clubs followed the rules and some didn't."
City chairman Khaldoon Al Mubarak said on Saturday he remains "confident" of proving their innocence, while chief executive Ferran Soriano is understood to have told the European Football Clubs board meeting in Copenhagen on Monday that City disagreed with the ruling but the club were still fighting.
