The Premier League champions face a wage cap on their players, a Champions League squad that will be restricted to just 21 players, a limit of £49million net spend in the upcoming transfer window and a record £49million fine for breaking the Financial Fair Play regulations.
The club have decided against contesting UEFA's sanctions but, despite accepting the charges, Khaldoon is adamant City's financial model is not one that should be scrutinised, with the club free from debt.
"We have a sustainable project today, in Manchester and across the board in the City Football Group," Khaldoon told the club's official website.
"We have zero debt. We don't pay a penny to service any debt. For me, that is a sustainable model.
"However, our friends at UEFA seem to believe otherwise. They have their view, we have ours.
"I disagree with their views, but we are pragmatic and one thing our fans need to know, we will do, as always, what is best for this club and the fans and if that means sometimes we have to take a pinch, we will take a pinch and move on."
Khaldoon also revealed City are on course to break even this year and make a profit next year, meaning they will avoid much of the substantial fine imposed on them.
And he insists all of this is part of the plan the club's owners started six years ago, believing their investment is going a long way.
"Six years ago we started a journey of investment. We invested in the club and in Manchester - the club was 20th in terms of revenue among clubs in Europe," Mubarak added.
"It was very challenging and had a lot of debt, poor infrastructure and difficulties attracting talented players to compete to win leagues domestically and in Europe.
"Over six years, step by step, we have invested in this club, in the stadium and in the best youth facilities in Europe that will come onstream this year as we try to see the success of our commitment to youth.
"This has been a strategy, to invest in top players from around the world, good players, talented players, good people.
"This year, we will break even and next year we will go into profitability, while maintaining everything I mentioned. We will keep investing in the club at every level - we will keep investing in youth."